Revenue says the online application system for the 'Help-To-Buy' scheme is "robust and working correctly."
A number of homeowners have been ordered to repay up to €20,000 to the agency after they were mistakenly approved for the scheme.
Revenue says the scheme's online application form is self-assessed - with "targeted checks" later revealing that some people had entered incorrect details online.
The agency says it will "take a reasonable approach" to recovering the money - provided households agree to pay it back.
A number of first-time buyers who qualified for the Help To Buy scheme have been ordered to pay the money back.
Over 6,000 people were awarded the grant of up to €20,000 to help fund a newly built home, but a Revenue audit has found that some did not meet the requirements.
The Help To Buy scheme was introduced in 2016 to encourage the construction of new homes and help people get on the property ladder.
New figures have found that over 6,000 people used the scheme to claim a tax rebate equal to 5% of the value of the home they were buying.
But despite originally approving the grants, Revenue has now run a series of follow up checks and found that some people did not actually meet the requirements.
In some cases interest of €110 a month will be added to the affected mortgage holders bill if they cannot pay the money back within three months.