Mahoney has called for a House Ethics Committee investigation of his own conduct and said he would be cleared of wrongdoing. House Speaker Nancy Pelosi also called for an investigation.
The FBI is looking into whether Mahoney hired the first mistress - and put her on the federal payroll - so she wouldn't reveal their affair, the person said.
The woman, Patricia Allen, has not returned repeated calls.
Mahoney, 52, who is married with a child, began his affair with Allen, 50, in 2006 while campaigning for Congress.
He won that year while promising to return morals and family values to Washington after Republican US Representative Mark Foley resigned amid revelations that he sent lurid Internet messages to male teenage pages who had worked on Capitol Hill. Foley was later cleared of criminal wrongdoing.
Mahoney hired Allen to work first for his congressional office, then his campaign. Campaign staff said she was later fired for performance issues, not because of the affair.
Allen then threatened to sue Mahoney for sexual harassment, they say.
Mahoney reached a settlement to avoid a public airing, paying her and her lawyers $121,000.
Mahoney's campaign staff says Mahoney paid the settlement to Allen with his own money, not with campaign funds or federal dollars.
Allen and Mahoney signed a confidentiality agreement that prohibits them from discussing details.
The FBI is also looking into whether Mahoney helped Martin County secure a $3.4 million reimbursement from the Federal Emergency Management Agency for hurricane damage in exchange for sex with a county official in 2007, the federal law enforcement official said.
The funds were approved late last year. A Martin County news release at the time noted "Congressman Tim Mahoney was instrumental" in helping secure the funds.
The second affair was confirmed by a person close to Mahoney's campaign who spoke on condition of anonymity because he was not authorized to discuss Mahoney's private life.
