It said the Home Affairs Secretary Caspar Tsui, the oath administrator, found the validity of the seven’s oaths questionable.
The seven councillors are Clarisse Yeung and Leung Pak-kin from the Wan Chai district council, Wei Siu-lik, So Yat-hang, Chan Wing-tai and Lai Tsz-yan from Eastern district, and Southern district’s Michael Pang.
Yeung and Pang have both been charged with violating the national security law by taking part in a primary election organised by the pro-democracy camp last year. Both were able to take their oaths in person as they had earlier been released on bail.
Leung said on social media that he received a letter from the authorities and has until 5pm on Monday to reply.
The other 17 Hong Kong island councillors who turned up at the oath-taking ceremony could keep their seats.
The only Hong Kong island councillor who didn’t show up, Peter Choi, meanwhile, has been disqualified with immediate effect.