A report said that even after Ryan Zinke said he would break ties with a foundation involved with the project, he continued working with the organization.
"Mr. Bernhardt has represented mining and extraction companies, developers, and oil and gas interests," wrote 150 environmental advocacy groups in a letter.
"This is as much about mismanagement over time," Zinke said, backing Trump.
The Hatch Act bars government employees from engaging in politics while on duty or in federal buildings.
"As representatives of the American taxpayers, we are responsible for ensuring that their hard-earned money is not wasted."
Department of the Interior just the latest in Trump's administration to face such criticism.
The former Montana congressman and Navy SEAL has faced plenty of questions about his air travel as secretary of the interior.
Department of the Interior raises a flag whenever Secretary Ryan Zinke is in the building.
Ranchers and tribal leaders alike are taking a stand against Secretary Zinke's rollbacks.
Environmental groups decried Ryan Zinke's announcement.
The new measures signed by Trump seek to gut most of the climate change regulations put in place by President Barack Obama.
The Northern Cheyenne Tribe said the administration lifted the moratorium on coal leases without hearing the tribe's concerns about the impact the coal-leasing program has on the tribe.
The department manages about a fifth of the country's surface, including national parks, forests and tribal territories, from the Arctic to the Gulf of Mexico.
The Interior Department oversees territories covering a fifth of the United States' surface from the Arctic to the Gulf of Mexico, including sensitive wildlife habitats, iconic landscapes, rich deposits of oil, gas and coal and important pasturelands for ranchers.
A congressman and former Navy Seal, Zinke may be Trump's most interesting and unpredictable Cabinet choice.
It remains unclear where Zinke would stand on opening up more federal lands to increased drilling and mining.