Last week Senator Thomas Carper, a Democrat from Delaware, wrote a letter to the E.P.A. inspector general requesting an investigation into allegations that Ms. Dravis did not attend work or perform her duties for most of November, December and January while continuing to draw a salary. The March 28 letter, obtained by The New York Times, said the information “raises questions” about whether the agency is adhering to internal rules regarding employee time and attendance.

A spokesman for the E.P.A. inspector general, Jeffrey Lagda, confirmed that his office has received the request and said he could not comment on whether the agency has taken up the investigation.

Jahan Wilcox, a spokesman for the E.P.A., disputed the allegation. “It is completely baseless and absurd to assert that someone with her responsibilities and office would have been away from her duties and responsibilities for months at a time as alleged,” Mr. Wilcox said in a statement.

Last week, when questions arose about Mr. Pruitt’s 2017 lease — in which he rented a room for $50 a night from the wife of J. Steven Hart, an energy industry lobbyist — the E.P.A. made public a finding by the agency’s ethics counsel stating that the price Mr. Pruitt paid for the use of the apartment was reasonable market value.

However, in the follow-up memo, obtained Thursday by the Campaign Legal Center, a watchdog group, the same in-house lawyer said he did not have all the facts when making his initial assessment of the lease. In a second memo he also released a copy of the lease, which shows Mr. Hart’s name crossed out and the name of his wife, Vicki, inserted.

Walter J. Shaub, a senior ethics official under President Barack Obama, said the original ethics opinion had been predicated on the understanding that Mr. Pruitt was leasing only one room in the apartment. But since then, there have been reports that Mr. Pruitt’s daughter stayed there while she was a White House intern.