The minister's comments were made after the Irish death toll from the ISIL terror attack in Tunisia climbed to three last night.
A married couple from Athlone, Laurence and Martina Hayes, joined Meath woman Lorna Carty as the Irish victims of Friday's atrocity in the resort of Sousse.
The minister offered his condolences to the families and loved ones involved and expressed his "appreciation" and "congratulations" to the gardai "who have been particularly helpful both in the Midlands and in Dublin".
"It is a very difficult times for the families and loved ones of those concerned. Our people are working in difficult and challenging circumstances on the ground," Minister Flanagan said in the radio interview.
Laurence and Martina Hayes, who were in their mid to late 50s, were on holiday in the resort when they were among the 38 murder victims of terrorist Seifeddine Rezgui, a student not previously known to authorities.
Laurence, known as both Larry and Lonnie to his friends, was a Bus Eireann inspector based in Athlone and a popular figure in the town where he was born.
His wife, Martina, was a stay-at-home mum and originally came from a large well-respected farming family in Kiltoom, Co Roscommon, not far from Athlone.
The couple have one daughter, Sinead (30), and lived in West Lodge, an estate on the western side of the Shannon in Athlone. They had moved into the house in the last couple of years.
Laurence's close friend, Willie Collins, said: "You could not ask for a nicer friend and colleague. I know that's something that's often said but it couldn't be more true.... I only met him 10 days ago and he told me he was going on holidays. It's just unbelievable. Larry was a great friend, a brilliant friend."
Hundreds of holidaymakers have been leaving the Tunisia beach resort where at least 38 people were killed in a gun attack on Friday.
The first inkling that the Irish death toll had risen came with a statement from the Minister for Foreign Affairs, Charlie Flanagan, around 4pm yesterday. It said: "In addition to the fatality made known yesterday, I can confirm that there is grave concern for two other Irish citizens who had been at the scene of the attacks at Sousse, Tunisia.
"The process of full and formal identification of victims is continuing in Tunis and will take a period of time before it is completed. The Irish Ambassador and Consul are on the ground in Tunisia, working closely with the Tunisian authorities," the statement said.
Gardai in Navan escorted Lorna's distraught son, Simon, to the airport on Friday where he flew out last night to be at the side of his father, Declan. Hazel was understood to have made the long journey home via Shannon Airport yesterday from the Turkish seaside resort.
Last night, the small community of Robinstown was reeling that one of their neighbours had died in such violent and unexpected circumstances.
Fr Noel Horneck, the priest in the neighbouring parish of Dunderry, said he heard the news of Lorna's death on his answering machine on Friday evening.
"The community is stunned and shocked," he said yesterday. "Simon has gone out there last night to his father. Hazel was away on holidays. Declan's brother is on holidays in the US."
Fr Horneck said he knew Lorna well, "as a parishioner, as a wife, as a mother. What can I say about a mother? She was just such a lovely person.
"Everybody is just so shocked at the moment."
Tributes and condolences flooded in from various local GAA clubs as news of Lorna's death spread through the community. Lorna's son, Simon, is a prominent local GAA player, who is on Mick O'Dowd's Meath panel.
Lorna, who worked as a nurse in Bedford Medical Centre in Navan, was actively involved in the local Dunderry GAA club, where her husband also serves as treasurer.
Last night, Dunderry GAA club postponed the senior and junior hurling matches that were due to take place this weekend.
The club issued a statement paying tribute to Lorna.
"Our thoughts and prayers are with the family of Lorna Carty. Lorna was always there to give a helping hand with all of our teams and events. She was greatly loved in our community and will be dearly missed."
A 19-year-old GAA player at the James Connolly club in Birmingham was named as one of those killed in Friday's attack. English-born Joel Richards from Wednesbury in the West Midlands, a student at the University of Worcester, also represented the Warwickshire county Gaelic Football side at inter-county level.
A statement from the James Connolly GAA club last night said "We are devastated by the death of Joel Richards. Joel was an exceptionally talented footballer, who represented both club and county with conviction on numerous occasions. He will be sadly missed."
Mr Richard's grandfather Patrick Evans and Uncle Adrian Evans were also killed in the devastating attack.
As a mark of respect GAA clubs in Birmingham will hold a minutes silence before games scheduled to take place today.
Speaking to the Sunday Independent, Sunway travel managing director Tanya Airey confirmed that 80 of the 112 holidaymakers who returned on the Aer Lingus flight from Tunisia last Friday night were customers of her company. Ms Airey said a number of Sunway holidaymakers had opted to stay on notwithstanding the events which had unfolded earlier that day.
Asked if Sunway had made a call on whether to allow intending customers due to depart on next Friday's flight to Tunisia to proceed with their holiday plans, Ms Airey said that a decision on this would be made early this week.
"Obviously we will be guided by the advice of the Department of Foreign Affairs. As of now, the department is not advising people against travelling to Tunisia. Our representatives on the ground are in the process of getting as much information as possible about the situation."
Ms Airey said that whatever decision was arrived at, a flight would still be going to Tunisia next Friday for the purposes of transporting holidaymakers who are due to return home on that day.
Meanwhile, survivors of the Tunisian beach resort terrorist attack are still reeling from their ordeal after the gunman disguised as a tourist opened fire on unsuspecting holidaymakers.
Elizabeth O'Brien, a paediatric nurse and mother-of-three from Dublin, said she will never forgot the terrifying sound as the shots from the Islamic terrorist's Kalashnikov rang out just a couple of hundred metres away from where she was sitting.
Ms O'Brien was soaking up the sun on the idyllic turquoise beach with other Irish and British holidaymakers at the Imperial Marhaba resort in Sousse while her sons, Spencer (11) and Jordan (13), frolicked in the water when the shots rang out in rapid-fire succession.
"It was so, so clear. It was like someone had let something off beside me," she told Sunday Independent columnist Brendan O'Connor, who hosted yesterday's Marian Finucane show on RTE Radio One.
She initially mistook the shots for a firecracker going off but soon realised it was a machine gun and immediately sprang into action.
She frantically began waving at her sons to get out of the water, who "had heard the same sounds I had," despite her eldest son initially dismissing the noise as a jet-ski backfiring.
But when they saw the expression on her face and her frantic hand gesture mimicking someone holding a gun, they knew it was serious, she told RTE.
"They didn't do anything, they just followed me. They kept running, kept running, they didn't ask me any questions, they didn't cry," she said.
Ms O'Brien then tried to alert other holidaymakers, many of whom were blissfully unaware of the cold-blooded massacre that was unfolding.
"I just ran to my children and grabbed our things and was running towards the hotel. I kept trying to tell Russian and Hungarian tourists to run but they didn't understand what I was saying and looked at me like I had 10 heads," she said.
She then fashioned her hand into the shape of a gun, while shouting at them "they're shooting, they're shooting, run!"
Waiters and hotel security staff also started screaming at the tourists to run from the beach, she recalled.
Even even after she reached their bungalow hotel room, Ms O'Brien said she didn't know what other horrors might unfold.
But she put on a brave face for the sake of her children.
"We got to our room and I closed the door and I said 'boys, we're going to be safe, we're going to be fine. We pulled the curtains. I said 'don't you put on the air conditioning, don't say one word. My youngest son put his hand to his head and said 'Mum, we've just got to get home'."
Meanwhile, Marion King, a 53-year-old mother-of-two from Lucan, Co Dublin, who also survived the attack, said the enormity of the massacre only really sank in when she arrived home on Friday night along with Ms O'Brien and other Irish holidaymakers,
"I'm really tired and relieved, and it's just starting to hit me today," she told the Sunday Independent yesterday.
"But it was completely surreal and very, very frightening."
Minister Flanagan advised any Irish citizens still in Tunisia who "wishes to come home and cut their holiday short" to liaise with tour operators on the ground and also with the consular assistance of the Department of Foreign Affairs.
"I would urge Irish citizens heading there and those in Tunisia to remain extremely vigilant and following any instructions given to them by police by their hotels and anybody wishing to plan a holiday in the immediate vicinity of the region I would ask that extreme caution be exercised at all times," he said this afternoon.
"I'm not in the business of imposing travel bans but I would say to people to be extremely vigilant. There is an on going review and monitoring of the security situation with intelligence agencies and the police in Tunisia as indeed is the case in other countries."