Liz Bowman, an EPA spokeswoman, said the agency was "addressing GAO's concern, with regard to Congressional notification about this expense, and will be sending Congress the necessary information this week".
The Government Accountability Office said the EPA violated the Financial Services and General Government Appropriations Act.
The agency spent $43,000 for installing the privacy booth in Pruitt's office, one of a number of expenditures for which the administrator is under scrutiny from Congress.
Under federal law, Presidential appointees are allotted $5,000 to decorate their offices, unless Congress is notified in advance about a higher level of spending.
The GAO report also said that it concluded that the EPA was in violation of the Antideficiency Act because the agency "obligated appropriated funds in a manner specifically prohibited by law".
US accuses Russia, Syria of tampering with Douma evidence
He spoke as the Organisation for the Prohibition of Chemical Weapons (OPCW) watchdog held an urgent meeting. Russia's deputy foreign minister said the delay was due to the Western strikes.
The GAO had been asked to investigate the matter by Democratic lawmakers including U.S. Senators Tom Carper and Tom Udall. "EPA must give a full public accounting of this expenditure and explain why the agency thinks it was complying with the law".
Pruitt, who was Oklahoma Attorney General before taking the EPA job, has been under fire for his spending on travel, security detail and renting a room in a condo owned by a lobbyist's wife for $50 a night.
The committee also is asking to meet with Chmielewski and Perrotta; Ryan Jackson, Pruitt's chief of staff; Millan Hupp, an aide; and Sarah Greenwalt, senior counsel to Pruitt.
"We have responded to Chairman Gowdy's inquiries and we will continue to work with him", EPA spokesman Jahan Wilcox said by email. Included in that amount was a $36,000 military flight so Pruitt could join President Donald Trump at a Cincinnati event, then make it to NY in time for his flight to Rome.