Wales Air Ambulance Charity is estimating an end-of-year loss of £2 million as a result.
The charity needs to raise £6.5 million every year to operate the service, with each mission on average costing £1,500.
Each year its helicopters attend around 2,500 missions, covering rural countryside and the country's bustling towns and cities.
That includes the length of the Welsh coastline and across its vast mountain ranges.
Bosses say the pandemic has been particularly challenging, but have thanked supporters who have found ways to raise funds during the lockdown.
Steven Stokes, Wales Air Ambulance head of communications, said: “As you can imagine, for fundraising and medical reasons, this has been a challenging period for us.
"There was an initial reduction in medical calls outs during the first month of the lockdown as people stayed at home but our mission count is now back to normal for this time of year.
“In terms of fundraising, there are many public and face-to-face events that generate funds for us – particularly at this time of year.
"We also have our shops across Wales. These activities needed to be stopped to prevent the spread of this awful virus but our ability to raise funds for our lifesaving service has been severely affected.
“We have been running an emergency appeal and our supporters have been incredible, finding innovative ways to raise money for us during the lockdown. We cannot thank them enough.
“Since the beginning of March, we have seen a 50 per cent drop in donations and we are estimating an end-of-year loss of £2 million.
"We are also mindful that the effects of the pandemic will be felt for some time and this shortfall in donations will continue in the next financial year.”
The charity has four airbase operations in Caernarfon, Llanelli, Welshpool and Cardiff.
It does not receive direct funding from the Government and relies entirely on the public's support.
Visit www.walesairambulance.com for more information and to donate.