NHS staff in England have been allowed to park for free since the start of lockdown, thanks to funding from the Department of Health.
The move came after more than 400,000 people signed a petition calling for the charges to be lifted for healthcare workers.
NHS Trusts set their own parking charges, but the Government said it would cover the cost of any income lost from daily fees paid by staff.
But ministers have confirmed to the i newspaper that charges will be reintroduced as emergency measures "cannot continue indefinitely".
Health minister Edward Argar said: "The provision of free parking for National Health Service staff by NHS trusts has not ended and nothing has changed since the announcement on March 25.
"However, free parking for staff has only been made possible by support from local authorities and independent providers and this support cannot continue indefinitely."
A date has not been set for the reintroduction of parking charges, but a spokesperson for the Department of Health told the i newspaper: "We want to make sure NHS staff can travel safely to work during the pandemic, which is why we requested that the NHS make parking free for staff, and that local authorities do the same with their car parks.
"As the pandemic begins to ease, the NHS will continue to provide free hospital car parking to key patient groups and NHS staff in certain circumstances. We will provide further updates on this in due course."
Mr Argar said the Government wants to be able to make good on its promise of free hospital parking for the disabled, frequent outpatient attendees, parents of sick children who are staying overnight and nightshift workers.
"Implementation of this commitment has been on hold whilst the NHS has been managing the Covid-19 pandemic and devoting its hospital parking capacity to staff and other facilities necessary for managing the pandemic," he said.
Trade unions are calling for free parking for all staff to be made permanent.
Sara Gorton of Unison, which represents nearly 500,000 NHS employees, said: "Nurses, cleaners and other health workers shouldn’t be punished for simply parking at work so they can save lives and care for patients.
"The virus problems are far from going away and when this is over, the Government should fund trusts properly so they can scrap staff charges for good."
Meanwhile, Liberal Democrat leadership candidate Layla Moran has called for clarity and said NHS workers must not be "saddled with extortionate parking charges".
"Removing parking charges for staff at the outset of Covid-19 was the right move," she said. "Our healthcare workers deserved to have certainty that they could get to work without extra charges or hassle.
"Now the Government must provide clarity and ensure our workers are not saddled with extortionate parking charges. We also need to see more efforts to promote green transport options for our healthcare workers."
Following the announcement in March, NHS chief executive Sir Simon Stevens said the move would make a "big difference" for thousands of frontline healthcare workers.
"Our NHS staff are working round the clock gearing up to deal with this unprecedented global health threat, which will be a major challenge for health services across the world, and we have listened to what they have told us would make their lives easier," he said at the time.