SIA's move will take effect from Saturday, while Scoot will stop carrying transit passengers from Singapore from April 30.
"From April 17, 2021 until further notice, Singapore Airlines will stop carrying transit passengers on our services from Singapore to Hong Kong due to new regulatory requirements in Hong Kong.
"Services from Hong Kong to Singapore remain unaffected, and passengers originating from Hong Kong will be allowed to transfer through Singapore Changi Airport en-route to their final destinations," said SIA, in response to queries from CNA.
"We will be reaching out to all affected customers to offer the necessary assistance," said the airline.
Customers may choose to rebook or seek a refund, added SIA.
In response to queries from CNA, Scoot also said that the airline would also stop carrying transit passengers on its flights from Apr 30 "until further notice".
"Customers who have booked transfer flights to Hong Kong will be provided a refund," it said.
"Our flights from Hong Kong to Singapore remain unaffected, and passengers originating from Hong Kong will be allowed to transfer through Singapore Changi Airport en-route to their final destinations."
Currently Singapore Airlines (SIA) passenger flights departing from Singapore have been barred from landing in Hong Kong from April 3 to April 16.
Scoot passenger flights leaving Singapore will not be allowed to land in Hong Kong from Friday to April 29, the government of Hong Kong said earlier on Thursday.
The temporary ban on SIA flights into Hong Kong was as a result of a passenger on SQ882 flying from Singapore to Hong Kong on March 31 being confirmed to have the coronavirus disease when tested on arrival in the territory.
In addition, three passengers had also "failed to comply with requirements specified under the Prevention and Control of Disease (Regulation of Cross-boundary Conveyances and Travellers) Regulation (Cap. 599H)", the Hong Kong government previously said.
According to a Hong Kong government website on coronavirus disease, the requirements prescribed by Chapter 599H are quarantine-related.
Thursday's press release from the Hong Kong government stated that a Scoot passenger flight (TR980), arriving from Singapore to Hong Kong on Apr 11, had two passengers who tested positive for coronavirus disease.
One passenger had also failed to comply with requirements “specified under the Prevention and Control of Disease (Regulation of Cross-boundary Conveyances and Travellers) Regulation (Cap. 599H),” said the release.
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