"Today I'm identifying houses of worship - churches, synagogues and mosques - as essential places that provide essential services," Mr Trump said during a hastily arranged press conference.
The president said if governors do not abide by his request, he will "override" them - but it is unclear what authority he has to do so.
The Centres for Disease Control and Prevention (CDC) had prepared reopening guidelines for churches and other houses of worship weeks ago, but the White House refused to release them until Thursday when Mr Trump abruptly changed course.
"I said 'You better put it out.' And they're doing it," announced Mr Trump on Thursday.
It's not the first time Mr Trump has spoken out ahead of guidance from the CDC.
At the beginning of April the president announced a change in guidance on face coverings that differed from the draft proposals put forward by the US health authority.
The President was speaking at a Ford Motor plant in Michigan that has been repurposed to make ventilators to meet the demands of the coronavirus crisis.
"And they're going to be issuing something today or tomorrow on churches. We got to get our churches open," Mr Trump said.
The USA currently has the highest number of confirmed Covid-19 cases and the highest death toll from the virus, according to the World Health Organization outbreak dashboard.