The issue was expected to be the subject of a congressional hearing today.
A spokeswoman for the House Oversight and Government Reform Committee, M J Henshaw, said Federal Air Marshal Service Director Roderick Allison told the committee about the allegations within the last week.
The air marshals being investigated have had their security clearances suspended pending the outcome of an investigation, Henshaw said.
Allison was scheduled to testify about the case before the committee, led by Utah Republican Jason Chaffetz.
"If these allegations are accurate, they are obviously inappropriate for anyone, let alone air marshals charged with securing our skies," the Maryland Democrat said.
Allison did not mention the investigation in written testimony submitted to the committee.
A spokesman for the Transportation Security Administration, which oversees the Federal Air Marshal Service at the Homeland Security Department, said TSA will hold its employees accountable if allegations of criminal behavior or misconduct are substantiated.
The prostitution allegations were first reported by the online news outlet The Intercept.
Lawmakers have focused their attention on questionable behavior by federal law enforcement officials since a 2012 prostitution scandal involving the Secret Service.
The former head of the Drug Enforcement Administration also came under fire earlier this year amid allegations that drug agents attended sex parties with prostitutes while stationed overseas.
