The government will not allow a group of people to "hijack Air Malta", Economy Minister Silvio Schembri said on Friday,
He insisted that the airline had other employees, not just pilots, to safeguard.
The airline and its pilots are currently at loggerheads over a minimum income offered to all employees.
"It is unacceptable that a particular section tries to dictate the operation of a company. Air Malta is not responsible for just the pilots.
"I will not accept that a group of people hijack Air Malta. I am not pleased with the situation but the company will not be brought to its knees because of a group of people," Schembri said.
As is the case with most airlines around the world, Air Malta's strategy would have to change once the pandemic is over, the minister added.
Air Malta wants to lay off 108 of its 134 pilots after failing to reach an agreement with the union on how to reduce payroll costs in the wake of the COVID-19 outbreak.
According to Schembri, some of the pilots are not agreeing with the union and have approached him to say they are willing to accept the €1,200 basic monthly income on offer. The pilots' union has declined this offer.
On Wednesday Air Malta accused the pilots' union ALPA of an "appalling display of force" by attempting to get a higher pay for pilots "at a time of virtually zero revenue" for the company.
All commercial flights in and out of Malta were suspended on March 21, with exceptions only for humanitarian, cargo and repatriation services, grounding Air Malta's fleet.
ALPA reacts
In a statement on Friday afternoon, the pilots' union said it "sadly notes the ministers’ unfortunate choice of words when making public statements".
"In reality Air Malta flight crew have always carried out their duties as assigned by the company with diligence, efficiency and effectiveness," the union said.
It went on to criticise the airline for not only refusing "to entertain ALPA’s requests for a meeting" but also for instead resorting to informing the department of industrial relations (DIER) to slash the 30-day effective consultation period prior required prior to enforcing collective redundancies, to just 15 days.
"The airline implied the DIER to be allowed to lay off 80 per cent of its pilots by Tuesday, April 21. This confirms Air Malta management’s real intent, to not engage with the workforce, but to forcibly extract an agreement of a permanent nature as indicated in a communication to ALPA and the Union Of Cabin Crew where any doubts as to management’s bad faith in the negotiations, were laid to rest."
The union said that the airline's "lies and deceit" was clear from the outset on negotiations, when it had told the DIER that its plan had been put together "in consultation and agreement with all unions and associations."
It said it was still willing to meet the company CEO and "carry forward an equitable and effective process, whilst securing the uncertain future of Air Malta’s pilot workforce."