The FBI and Federal prosecutors in Brooklyn are investigating Gov. Andrew Cuomo’s coronavirus task force with a particular focus on his administration’s handling of nursing homes early in the coronavirus pandemic.

The investigation, first reported by the Albany Times Union, is in its initial stages. Subpoenas have been issued, the sources said.

The full scope of the investigation is not immediately clear, but the sources said there was a particular interest in nursing homes, which have been a source of increasing frustration for Cuomo.

An aide conceded the administration withheld the nursing home death toll from state lawmakers out of fear it would be used against the state by the Trump administration.

“He starts tweeting that we killed everyone in nursing homes,” Cuomo’s top aide, Melissa DeRosa, said of Trump on the conference call recording.

“He starts going after [New Jersey Gov. Phil] Murphy, starts going after [California Gov. Gavin] Newsom, starts going after [Michigan Gov.] Gretchen Whitmer. He directs the Department of Justice to do an investigation into us.

“And basically, we froze, because then we were in a position where we weren’t sure if what [numbers] we were going to give to the Department of Justice or what we give to you guys … was going to be used against us,” DeRosa told the legislators. “We weren’t sure if there was going to be an investigation.”

Cuomo conceded this week his handling of nursing home fatality data created a “void” that became filled by misinformation and conspiracy theories, but he declined to apologize.

“The void we created by not providing information was filled with skepticism and cynicism and conspiracy theories which fueled the confusion,” Cuomo said during a news conference Monday. “The void we created disinformation and that caused more anxiety for loved ones.”

The controversy over nursing home deaths has dogged Cuomo for months. At the onset of the pandemic, state health officials directed nursing homes to accept residents recovering from the virus as they were discharged from hospitals.

The directive was rescinded several weeks later, but Cuomo faced criticism that it contributed to a high level of deaths in nursing homes. The governor said he based the decision on federal guidance at the time and insisted staff members, not residents discharged from hospitals, brought coronavirus into nursing homes.

Cuomo said Monday that 98% of the nursing homes that accepted a patient from a hospital already had Covid-19 cases.

“Covid did not get into the nursing homes by people coming from hospitals,” Cuomo said. “Covid got into the nursing homes by staff walking into the nursing homes when we didn’t even know we had Covid.”