Twenty-five district councillors from Eastern, Central and Western, Wan Chai and Southern districts were told to take their oaths at North Point Community Hall on Friday.
Speaking after the closed-door ceremony, Home Affairs Secretary Caspar Tsui said only 24 councillors attended the event.
He said Choi didn’t show up and would not be given a second chance to make the pledge.
Tsui said decisions will be made later in the day as to the validity of the other councillors’ oaths.
Earlier, Choi announced on social media that he would not take part in the oath-taking ceremony.
He said he couldn’t pledge allegiance to a government that doesn’t focus on the people, adding that he had initially joined the council to monitor the authorities.
Several other councillors spoke to the press after attending the ceremony.
One of them, Victor Yeung of the Democratic Party, said he hadn’t thought too much about whether he would be disqualified.
Paul Zimmerman from the Southern district council told reporters he wasn’t worried about losing his seat, but didn’t see why the oath-taking ceremony was necessary.
“I’ve always done exactly what I said today. I uphold the Basic Law conscientiously, dutifully, and honestly. I’ve always done so and will always do so. So I don’t see a problem with this oath-taking,” he said.
“I thought it was superfluous, because we’ve already done it. When we stood for the election, we already made declarations. But we do it today again to reconfirm our position.”
Lawmaker and Wan Chai councillor, Paul Tse, meanwhile, said the ceremony went smoothly and there was no “drama”.
More than 260 district councillors have resigned in recent months, with some saying they didn’t agree with the oath-taking requirement, and others fearing they could be asked to repay salaries and expenses if they were disqualified.
The exodus of more than half of all of the SAR’s district councillors means many councils don’t have enough members to function.