The Taoiseach's criticised John Delaney's appearance at the Oireachtas Sport Committee.
The former CEO of the FAI appeared before the committee earlier this week, but did not answer any questions - citing legal reasons.
The committee had been looking for answers as to why he gave the FAI a €100,000 loan in 2017.
While President of the FAI, Donal Conway, told TDs and Senators that the FAI broke State funding rules by failing to tell Sport Ireland about the loan or any "material deterioration" in the association's finances in 2017.
Sport Ireland also announced it was to temporarily 'suspend and withhold' future funding to the FAI until the association can prove it is compliant with its funding rules.
Leo Varadkar says while Mr Delaney was within his rights not to fully engage, many people wanted the questions answered.
"I don't think anyone would be satisfied by it - I think the public taxpayers, football fans would have liked to have seen those questions being answered.
"But the truth is he was within his legal rights not to answer those questions because he's not a public servant and therefore is not accountable to the Oireachtas."