The railway operator closed Po Lam and Hang Hau stations on the Tseung Kwan O Line just before 11.30 pm and Tai Wai station, on the East Rail and Ma On Shan lines, just before midnight.
Then after midnight, it closed Che Kung Temple and City One stations on the Ma On Shan Line.
On Tuesday, the MTR was criticised for closing around half of its stations as protests broke out across Hong Kong during China’s National Day.
MTR stations have frequently been the target of anti-government protesters since August. This is when the company began closing stations during protests after being accused by mainland media of helping protesters escape.