The troops have been sent to reinforce other UN posts in the ceasefire zone but have not encountered any armed troops.
All Defence Forces personnel and equipment remain safe and accounted for.
A statement from the Defence Forces this evening said 'there have been a number of engagements between armed elements in the Golan Heights in the last 36 hours'.
Details of the ongoing operations cannot be disclosed for operational security reasons.
The statement comes following the kidnapping of 43 UN peace-keepers, believed to be from Fiji.
No Irish soldiers are among the UN peacekeepers who were reportedly captured by Syrian militants this morning.
Currently, six countries contribute troops to the force: Fiji, India, Ireland, Nepal, Netherlands and the Philippines.
"The UNDOF Force Commander has deployed the Force Commanders Reserve, consisting of Irish personnel, in response to the current situation," the Irish Defence Forces reported this evening.
"For operational security reasons details of ongoing operations will not be disclosed."
Irish troops remain 'on high alert' this evening amid increased fighting in the area between Syrian Government forces and armed elements.
Meanwhile, Defence Minister Simon Coveney has said that the kidnapping of 43 UN peacekeeping troops is 'cause for review of the overall UN peacekeeping mission'.
The troops from the UN Disengagement Observer Force (UNDOF) all reported to be from Fiji, were reported to have been abducted during clashes in the Golan Heights area.
Heavy clashes have occured between Syrian government forces and militants fighting with the Al-Nusra Front, an al-Qaeda linked group.
The Defence Forces confirmed that all Irish troops are accounted for "but security remains heightened in the region".
“Ireland is very committed and has been an absolute centre of this mission. If the Irish were to withdraw the mission would collapse so I wouldn’t make that decision lightly," Minister Coveney told RTE Radio One's DriveTime programme.
“Right now we’re dealing with immediate instances, this isn’t the first difficulty troops have encountered in recent weeks.
“What needs to be called into question now is the overall objective of the mission, this was meant to be a peace-keeping mission but now UN soldiers are being caught up in a civil war.
“Those discussions need to happen in the context of the UN mandate linked to that mission," he continued.
“Our primary focus is to ensure our troops are safe and perform the role they’re trained to perform and to keep the mission focused and intact and make sure these 43 captured troops remain unharmed.
“Negotiations are going on at the moment. So there is a stand-off and clearly there are efforts being made to diffuse that situation.
“It is our understanding all 43 troops are still alive.
“I have very clear and detailed information on the Irish troops and where they are and their safety, but this is cause for us to review the overall mission once this situation is resolved.”
Minister Coveney explained that the 130 Irish troops based in the region 'are a very well-armed mobile unit that can move from various posts that the UN have in the Golan Heights to wherever they are needed'.
“The purpose of this mission was to act as a buffer strip between Israel and Syria to reduce the likelihood of rocket fire across the border, a lot like what our troops did in southern Lebanon," he explained.
“Unfortunately what has happened is the free Syrian army and the Syrian armed forces are fighting a very nasty and bitter civil war. This war has been impacting on the UN’s position quite seriously.
“Two of these UN posts armed by Fijian forces were essentially over-run by rebels in Syria."
Mr Coveney added that the 43 troops were disarmed and, although other posts have been threatened since, no arms have been handed over.
“This is a situation that has been changing by the hour today," he said.
“I can and I think it is important to say to the family and friends of Irish troops in the Golan heights who are performing an important peace-keeping role that the Irish troops are safe and indeed none of the UN troops have lost their lives."
The UN are currently in negotiations to secure the soldiers' release.
Meanwhile, the Syrian government denounced the "kidnapping" of the peacekeepers.
In a statement issued by the Syrian Foreign Ministry, the government said it holds "the terrorist groups and those who support them fully responsible for the safety of the UN peacekeepers, and calls for their immediate release".
Heavy fighting has engulfed the Syrian side of the Golan since yesterday, when rebels captured a crossing on the disputed frontier with Israel. A rebel spokesman said the opposition is focused on fighting President Bashar Assad, and poses no threat to Israel.
Today, government planes targeted several rebel positions in the area, including in the village of Jaba, the Observatory said. The Local Coordination Committees, another activist group, also reported the air raids.
The Observatory said heavy clashes were raging between the rebels and the Syrian military in Jaba and the surrounding countryside.
White plumes of smoke set off by exploding mortar rounds could be seen on Thursday from the Israeli side of the Golan. The sound of small arms fire could be heard echoing in the background.
UN spokesman Stephane Dujarric said the 43 detained peacekeepers are from Fiji and are thought to be in the southern part of the area of separation.
The 81 troops from the Philippines had their movements restricted.
"The situation is extremely fluid. Obviously, we are very concerned," he said.