Three passengers on the March 31 flight also failed to comply with requirements specified under the Prevention and Control of Disease Regulation, Hong Kong authorities said on Friday.
Singapore Airlines confirmed the order but said passenger services from Hong Kong to Singapore would not be affected. The suspension applies until April 16.
The airline said pilots and cabin crew on three international flights from Singapore to Jakarta, Bangkok and Phnom Penh had received both of the required doses of the Pfizer-BioNTech vaccine.