British Airways refused to attend a meeting with Home Secretary Priti Patel on Thursday to discuss the UK's new quarantine plans.
The UK's biggest airline is a fierce opponent of the plans, which will require travellers to the UK to isolate for 14 days or face a £1,000 fine.
BA did not give a reason for its absence and declined further comment.
But a Whitehall source told the BBC it was clear BA was not serious about getting "Britain moving again".
The new quarantine rules come into force from 8 June. BA, under huge financial strain due to the pandemic, has called it "another blow to our industry".
BA and owner IAG - which also runs Iberia and Aer Lingus - are understood to be annoyed at what they see as a lack of consultation over the quarantine's introduction.
EasyJet and Virgin Atlantic, as well as the owner of Heathrow Airport, were among the aviation businesses that attended the telephone meeting with Ms Patel and junior aviation minister Kelly Tolhurst. The Home Office said 24 representatives from the aviation, maritime and rail industries were on the call.
The home secretary told the meeting it was important for everyone in the transport sector to help "safeguard our [economic] recovery" and "protect passengers and the whole country from a second wave of coronavirus".
However, an industry source said that BA feels "it has not been treated professionally; that the meeting was a waste of time".
A Whitehall official hit back, telling the BBC: "It's a shame that British Airways don't want to directly make their case to the home secretary and the aviation minister. Clearly they are not serious about working with the government to get Britain moving ."
BA has faced heavy criticism in parliament in recent days over a plan to slash jobs while accessing the government's furlough scheme.
In April, BA said it would cut 12,000 roles and weaken terms and conditions for its remaining staff, just weeks after it had put 30,000 workers on the job retention scheme which pays workers' wages.
The airline has defended the cuts as necessary, but on Wednesday Ms Tolhurst suggested BA should be held to account for what one MP called a "breach of faith".
"The [furlough] scheme was not designed for taxpayers to fund the wages of employees only for those companies to put the same staff on notice of redundancy during the furlough period," Ms Tolhurst said.
Aviation bosses are fuming about the quarantine. And tonight's conference call seems to have made things worse.
Most were apparently unimpressed, with one person present on the call even describing it as "a shambles".
They feel they got no reassurances from Priti Patel that the quarantine would be reduced in any significant way soon by agreeing so-called "air bridges". These are safe corridors between the UK and countries with low infection rates meaning people won't have to self-isolate after they travel.
That is an interesting contradiction in tone from other government sources who insist ministers are working hard to establish a number of air bridges, especially with European countries, as soon as possible.
The fact that BA's parent company IAG didn't even attend the call is the ultimate sign that relations between the government and UK aviation are at rock bottom.
The government insists the new quarantine rules will help contain the spread of coronavirus but has faced a backlash from Conservative MPs who argue they will harm airlines and stop people taking summer holidays
The rules have also been roundly criticised by the UK's tourism industry, which has all but ground to a halt due to the pandemic.
In her opening remarks at the meeting Ms Patel said: "Protecting lives will always be our top priority, but I am alive to the impact on your sector and I'm asking you to work with us on this."
But earlier on Thursday, the boss of the UK's biggest airport services company, Swissport, said on Thursday that the plan could deliver a "killer blow" to the tourism sector.
Michael O'Leary, chief executive of Ryanair, echoed those concerns, saying the requirement to self-isolate would "significantly reduce European visitors".
"The safety and security of our people and our customers is always our top priority and public health must come first," a Virgin Atlantic spokesman said.
"However, the introduction of mandatory 14-day self-isolation for every single traveller entering the UK will reduce customer demand significantly and prevent a resumption of services at scale."
On Monday, a group of 200 travel companies wrote to Ms Patel asking for the plans to be scrapped.
The letter suggested travel should be possible for people - without quarantine - between destinations "deemed safe from coronavirus".
So-called air bridges would allow visitors from countries where coronavirus infection rates are low into the UK, without having to self-isolate for two weeks.
A government source told the BBC there was a "list" of countries which the government was hoping to secure air bridge agreements with, which include all major European tourist destinations such as Portugal, Spain and France as well as Australia and Singapore.
However, for now the government's official position is that the idea is "under consideration", not established policy.