The work would be carried out at night so that flights are not affected, Nguyen Huy Duong, deputy director of the airport, said.
S3 was temporarily closed on August 9 on safety grounds, but was partially reopened on August 19, Noi Bai authorities said.
A section of the runway 1B also needs repairs, and so will only be used between 1 a.m. and 7 a.m. between September 11 and 13.
Potholes of up to a meter and cracks of 30-50 centimeters were found on the runway this month, the authorities said.