Trump was asked about the controversy surrounding Pruitt in a White House event Tuesday but only said: "I hope he's going to be great."
The EPA also did not provide details on the call.
More members of Congress on Tuesday called on the EPA's inspector general to look into the arrangement.
Members of Congress have requested new investigations into the deal including whether ethics officials had all the information when they issued a statement that the deal did not violate the agency's gift rules because Pruitt paid market value for the room, even though he only paid $50 a night for nights that he stayed in the room.
The ethics decision did not mention possible conflicts of interest, or allegations of conflicts of interest, that could arise from the administrator of the EPA living with a lobbyist tied to energy groups.
ABC News reported last week that Pruitt rented a bedroom in a Capitol Hill condo for much of his first year in Washington. The condo is co-owned by Vicki Hart, the wife of lobbyist J. Steven Hart who has registered to lobby for companies with environmental or energy interests.
Rep. Carlos Curbelo, R- Florida, weighed in on the controversy tweeting that Pruitt's corruption scandals are an embarrassment and that he should resign or be fired.
Another Florida Republican, Rep. Ileana Ros-Lehtinen, said in a statement and tweeted that someone should take over EPA amid all the scandal and distraction around Pruitt.
"I agree with my colleague, Carlos, that the EPA administrator should resign. When scandals and distractions overtake a public servant's ability to function effectively, another person should fill that role,” she said in a statement to ABC News.
Ros-Lehtinen is retiring from Congress this year.
In the letter Whitehouse cites guidance from the Office of Government Ethics that says government employees should consider declining a gift that may not technically violate gift rules if "their integrity or impartiality would be questioned if they were to accept the gift."
Reps. Ted Lieu, D-California, and Don Beyer, D- Virginia, also asked the inspector general to investigate in a letter on Tuesday.
The ethics memo stated that the lease authorized the use of the condo by Pruitt and his immediate family, including his daughter McKenna Pruitt who stayed in a second bedroom during a White House internship.
But Vicki Hart previously told ABC News that she was not aware of other people using the bedrooms or living quarters and did not give permission for that.
"The OGC decision and Hart’s statements cannot simultaneously be true. This discrepancy is further evidence of the need for the EPA Inspector General to conduct an investigation to determine if misconduct or mismanagement led to said OGC decision, and whether the Ethics Office was influenced in any improper manner," Lieu and Beyer wrote in the letter.
On Monday Democrats from the House Energy and Commerce Committee also asked the EPA to provide more information about the rental agreement. Republicans on that committee also said they have asked the EPA for more information.
The inspector general's office confirmed that they have received the letters and that he and his leadership team are reviewing the requests.
ABC News' Trish Turner contributed to this report.