"No matter how much Scott Pruitt likes chick-fil-A, it is strictly forbidden for public officials to use their public positions for the private gain of others, such as supporting their products," Evers said.
Mr. Pruitt, in a statement on Wednesday, called Millan Hupp a "valued member of the E.P.A. Team" and a "colleague, friend and trusted partner."
Jahan Wilcox, a spokesman for E.P.A., did not comment on Ms. Greenwalt's departure. Two former agency officials who wanted to remain anonymous to talk about staff confirmed that they had submitted their resignation.
Senator John Kennedy of Louisiana said Mr. Pruitt acts "like an idiot."
"I think he's hurting his boss, and if he's hurting his boss, he's hurting the American people," Mr. Kennedy said.
But Mr. Pruitts boss, President Trump, seems to be satisfied.
"Thanks, Scott, a lot, E.P.A. is really doing very well and you know, someone has to say that a bit about you," Mr. Trump told him during a briefing on the upcoming hurricane season. "People are very impressed by the work being done at E.P.A. Thank you, Scott."