Gardai are investigating Athlone Town AFC amid allegations of match-fixing and irregular betting patterns.
Officers from the Garda National Economic Crime Bureau (GNECB) - previously known as the Garda Fraud Squad - are investigating the matter.
It is understood the GNECB became aware of the matter in the last 24 hours, after the FAI handed over a file from Uefa, which alerted it to irregular betting patterns.
The FAI has also launched an investigation into the midlands Airtricity League First Division club.
Both investigations were triggered by activity surrounding the match between Athlone and their neighbours Longford Town last weekend.
Athlone lost the game 3-1 and it is believed that a late goal scored by Longford is one part of the investigation.
Uefa contacted the FAI to point out unusual betting patterns in international markets and has presented detailed analysis on the subject.
The FAI has handed a copy of the report onto the GNECB, which will launch a criminal investigation into the matter.
Separately, the FAI will commence interviews with players, coaches and officials of Athlone from Monday.
If the FAI finds that a breach of rules has occurred, charges will be issued and the matter passed onto the FAI's disciplinary panel.
Athlone's erratic start to the campaign had become a discussion point in Irish football circles.
They were taken over by foreign investors over the winter, but mystery surrounds their identity, with the club refusing to disclose their details.
An FAI statement suggested it has been keeping tabs on Athlone across the campaign.
"The FAI has been monitoring the club since it received information from Uefa following an inquiry by FAI competitions director Fran Gavin, prior to the start of the 2017 season," the statement said.
"On March 29, Mr Gavin delivered an integrity workshop presentation to the Athlone Town AFC senior squad and coaches on the prevention of match-fixing and betting, in his role as FAI integrity officer."
The FAI have also written to Longford Town, but its statement made it clear that Athlone are the focus of the probe.
A statement from the board and the management committee of Athlone Town AFC said they were "absolutely shocked by the contents of documentation forwarded to us by the FAI and Uefa" concerning the Longford match.
"The club absolutely abhors match-fixing and would never knowingly get involved in such unacceptable activity," they said.
The club added they will co-operate with both investigations and would not be making any further comment until they were concluded.
Athlone's takeover was followed by an influx of overseas players and confusion over the identity of their manager.
Local man Colin Fortune was listed as manager at the start of the season in February. Athlone won their first two matches under Fortune - but he was quickly replaced by Portuguese native Ricardo Monsanto.
Monsanto has since left the club, with another Portuguese coach, Ricardo Cravo, taking temporary control.
They sit second from bottom in the table and there has already been a high turnover of players.
It is understood that fewer than a dozen players attended one training session this week.
Mr Gavin said in an interview in March that Athlone were building a "unique project" and added that he had met the mystery owners.
"I have met the new investors in Athlone and they are quite ambitious," said Mr Gavin.
"We've never experienced that type of investment in a club where they're bringing players in from all over Europe. You wonder about their motivation, so that's something we've to look at very carefully.
"We would like to see the project being a success but we need to wait and see. It is important to make sure the club is going in the right direction."
Earlier this week, former Athlone Town boss Mick Cooke told Dublin's 98FM League of Ireland podcast that the current situation at his old club needed scrutiny.
"Nobody seems to know," Cooke said when asked what was going on at his former club.
"Even Colin Fortune is gone out of it, when you think of it, a club that has massive potential, a lovely stadium, fantastic ground, and the best of everything.
"They have new investors but nobody seems to know who they are, they've a lot of foreign players, where they came from or if they're going to college in Athlone, nobody seems to know what they're about.
"They're a mystery at the moment and something Mr Gavin will have to keep an eye on."