Taxpayers have paid more to protect Pruitt than past EPA chiefs but those expenses are justified since Pruitt has been under threat, Trump wrote.
"Scott Pruitt has received death threats because of his bold actions at EPA," Trump wrote.
The costs of Pruitt's security detail have come under scrutiny recently as have the costs of his travel and housing in Washington. Trump defended those costs, too.
"Rent was about market rate, travel expenses OK. Scott is doing a great job!" Trump wrote.
The head of a congressional oversight panel is investigating Pruitt's use of a condominium tied to an energy lobbyist, an aide said on Saturday. The House of Representatives Oversight Committee, chaired by Republican Representative Trey Gowdy, has begun looking into Pruitt's housing arrangements, according to the aide, who was not authorized to speak publicly.
On Friday, an EPA spokesman said Pruitt has faced "unprecedented" threats and security has been costly.
"Americans should all agree that members of the President's cabinet should be kept safe," said EPA spokesman Jahan Wilcox.
Gowdy's probe adds to the pressure on Pruitt, a vocal critic of mainstream climate change science who sued the EPA more than a dozen times when he was Oklahoma's attorney general.
Many Democrats and even a few Republicans have said he should resign or be fired.
Lawmakers have been scrutinizing Pruitt for renting a room in a high-end townhouse co-owned by the wife of energy industry lobbyist Steven Hart for $50 a night, an arrangement that has drawn fire from ethics experts. Media reports say the payment is less than one-third the price of similar properties.
Hart lobbies for companies regulated by the EPA. Pruitt is also under fire for frequent first-class air travel and for purchasing costly items for his office, including a soundproof telephone booth.
"I don't have a lot of patience with that kind of stuff," Gowdy said of Pruitt in a video released by the environmental group Friends of the Earth. "You've just got to be a good steward of public services."
As part of the committee's investigation, the EPA has produced documents, including a memo from the EPA ethics office that initially cleared Pruitt of accepting a gift from a lobbyist but did not address whether he broke other federal ethics regulations.
An administration official said Pruitt met with President Donald Trump on Friday morning, a week after White House Chief of Staff John Kelly advocated for Trump to fire him. Trump told reporters on Thursday that he would take a look into ethics allegations against Pruitt but added the official was doing a "fantastic job."