The decision to separate China aircrew from those working international routes was made in light of the emerging Omicron variant, sources said, as officials weigh even tougher rules and fewer exemptions for flight personnel, the South China Morning Post has learned.

The new measures, which come as Hong Kong rushes to meet Beijing's requirements for reopening the mainland border, will add yet more cost and operational complexity for city flagship carrier Cathay Pacific.

The airline is already pushing ahead with contingency measures that could see some of its pilots relocated overseas.

In a memo to staff on Wednesday night, Cathay general manager of operations Mark Hoey said the company was poised for the government to act on the new rules imminently.

"Expect the final decision on how our crew exemptions will be affected by these changes, if at all," said Hoey, who went on to say the airline had flown as many crew members as it could back to Hong Kong before midnight to beat potential new quarantine rules.

"Given the uncertainty that currently exists, we made the decision last night [Tuesday] that, until we have a decision and can adjust the operation accordingly, we will protect our crew as a priority," Hoey added.

In response, the Transport and Housing Bureau said: "We will continue to closely monitor the situation and will review the anti-epidemic measures for aircrew as and when appropriate."

Hong Kong, one of the first places to record an imported case of Omicron, has reacted dramatically to the situation - branding more than a dozen new countries as high-risk, or Group A, which requires a 21-day quarantine for arrivals and bars all non-residents.

The prospect of every region where Cathay operates, other than mainland China and Taiwan, being reclassified as Group A has grown rapidly in recent days as the government weighs how to react to the newly emergent variant.

Plans are also being advanced for airlines to arrange for Covid-19 testing for aircrew to take place in their homes so they will not need to enter the community at all during their medical surveillance period.

Hong Kong International Airport last month divided its airport departure and arrivals into two zones - one for mainland China and one for the rest of the world - to help the city bolster its case to convince Beijing to reopen the land border, the administration's top priority.

The separation includes separate Covid-19 arrival testing centres.

In a memo last week, Hoey discussed how the new arrangement would affect aircrew.

"[The government] only wants to put crew who haven't been to any other countries through the [testing centre dedicated to China] to keep the environment low risk. So unless we have dedicated mainland China crew, they will not allow the use of the new testing centre," he added.

Hong Kong has gone for months without a local infection under its tough zero-Covid strategy.

But the government's shifting rules amid the emergence of Omicron poses a grave threat to Cathay Pacific's ability to operate even a reduced flying schedule.

Cathay last week said it would slash its December flights into Hong Kong due to a shortage of available crew, converting the affected passenger flights into cargo only.

The airline operates what are known as closed-loop flights, meaning crew fly for three weeks at a time, then do two weeks of hotel quarantine on return.

The airline is also still dealing with the fallout from an incident in Frankfurt last month, when three pilots who contracted Covid-19 were dismissed for breaching company policy by leaving their hotel rooms overseas.

A spike in resignations has taken place over recent months, with a growing number of Cathay pilots reconsidering their long-term future working under the city's zero-Covid regime.

The latest aircrew rules, which took effect on Nov 26, extended quarantine exemptions for local cargo crew staying in Alaska, Australia, New Zealand, Singapore, South Korea, Japan and Thailand.

Aircrew flying from destinations deemed high risk must serve 14 days of quarantine, rather than the 21 faced by travellers.

Health officials also extended special dispensation until Dec 31 for aircrew staying in certain high-risk countries like the United States and the Netherlands that were among a group of 15 previously upgraded to high-risk.

Under that dispensation, those countries would be treated as medium risk, meaning crews would be subject to either seven days of quarantine or none at all.