The documents released through a Freedom of Information Act request by the Sierra Club and reviewed by CNN also show the hiring freeze affected an additional 140 people internally chosen for jobs or, in some cases, offered jobs but could not be finalized before the freeze went into place.
President Donald Trump's executive order meant that no vacant positions existing at noon on January 22, 2017, could be filled and no new positions could be created, except in limited circumstances. The administration said the freeze would remain in place until a plan was in place to reduce the federal workforce nationwide "through attrition."
The scientific positions left unfilled were particularly troubling for Sierra Club Global Climate Policy Director John Coequyt.
"That's about one-third of the total number of positions hiring was frozen for, so we are seeing high skilled people being held up from working at the agency," Coequyt said.
"These posts are crucial to understanding what types of pollutants are present, where they are coming from, how they are affecting people and wildlife, and how to return human and natural ecosystems to a healthful state. Every decision by the agency -- from permit approvals to regulations -- must be supported by extensive research," he added.
The positions impacted by the government-wide hiring freeze include more than 70 scientists and engineers in areas like the environment, physical science and life science -- and at least six law enforcement officers.
The Sierra Club believes the figures reported by the EPA are minimums. The environmental group says that's because in addition to freezing currently-open positions, the executive order prevented any new positions from being created. "The true number of EPA jobs held back by the administration could be dozens -- even hundreds -- more than the 351 being reported," a Sierra Club spokesperson said.
The EPA declined to say whether the positions will be filled now that the freeze has been lifted or whether it would leave the positions vacant to help achieve the White House's desired 31% reduction in EPA staff.
The EPA will continue to work to "maximize resources to protect our air, land, and water," administrator Scott Pruitt said in a statement.
The White House Office of Management and Budget did not immediately respond to a request for comment.
The Trump administration lifted the government-wide hiring freeze on Wednesday, but said "targeted" and "surgical" cuts to staffing across agencies is in store for the coming months. Agencies have until June to develop their plans, which are to be finalized by September.