Physical distancing would slash the capacity at Dublin Airport by 70% with passengers potentially facing huge queues into the car parks, according to DAA chief executive Dalton Philips.
But comments by the Republic's health minister Simon Harris suggesting foreign travel looked 'highly unlikely' for the rest of the year had not been helpful, he said in a video message to staff.
Passenger traffic at Dublin and Cork would fall to nine million this year and to between 20 million and 24 million next year compared to 36 million last year, he said.
An equivalent corresponding 35% cut in the workforce could put more than 1,000 airport jobs in jeopardy, said sources.
Philips told staff job losses at DAA were inevitable but he could not yet say how many staff must leave to "right size" the business.
The DAA boss said: "If we implement physical distancing in our airports, that separation of two metres, we reduce the overall capacity in the airport by 70%.
"We will have people queueing out the door and into our car parks with only a small level of traffic coming back.
"So we really have to get to the bottom of whether physical distancing will remain for airports or not.
"Because if it is not going to be applied on the aircraft there is a strong argument that says it shouldn't be applied in the airport."
Posing a number of questions about screening, Mr Philips said "But then the question is... where do you screen people?
"Do you screen people with vaccination passports before they even travel to the airport or do you do some sort of temperature or thermal checking as they come to the airport? As we look into 2021, traffic looks like it is going to be in the 20 to 23 or 24 million mark - very hard to land on a specific number.
"It doesn't help when we have things like the minister coming out at the weekend - Minister Harris - saying that he recommends that people don't travel and that there should be recommendations to stop travelling until the end of this year."
The comments came as senior Irish airline executives said that temperature checks, mandatory blood tests and significant changes to security and baggage systems at airports such as Dublin may be the only way for airlines to return to any form of normality in the absence of a Covid-19 vaccine.
With social distancing now seen as economically impossible on aircraft, a showdown over whether airlines or airports pay for extraordinary new screening measures is inevitable, sources said.