It says this affects trans-Pacific, European, Southwest Pacific, Riyadh and Dubai services cargo flights.
It also affects cargo-only passenger flights until January 6.
On Tuesday, the government announced that cargo aircrew will be required to undergo three days of hotel quarantine when they fly into Hong Kong.
The announcement followed the news that three Cathay Pacific cargo aircrew members who had recently returned from the United States had Covid-19.
The airline said the three-day quarantine requirement would lead to a drop in flight frequencies and would affect supply chains in the short term.
It also said the the measure would undermine the status of Hong Kong International Airport as a cargo hub.