Chief Executive Carrie Lam has denied claims that the government is cracking down on civil society, saying the police have simply been ensuring that no groups or individuals are able to endanger national security.
Critics allege that it is a crackdown by the authorities that has forced long-standing groups, such as the Professional Teachers' Union and the Civil Human Rights Front, to disband.
Asked about the claims and her view on the legal status of the Alliance in Support of Patriotic Democratic Movements in China, Lam said she disagreed with the use of the word "crackdown", when there is only law enforcement work by the police.
"We respect civic society. Hong Kong has large numbers of NGOs and think tanks and research agencies who are shouldering their civic responsibility in trying to improve Hong Kong's situation," Lam told reporters before the weekly Executive Council meeting.
"But where there are associations, whether they are registered or not registered, that exist in order to undermine Hong Kong's security, let alone to advocate independence or collude with external forces to harm Hong Kong and the country, that is not something we should condone."
The CE stressed that the police are correctly using their powers under the national security law to ask the alliance for information, including about its members and finances.
On the disqualification of Civic Passion's Cheng Chung-tai from the legislature, Lam said the specific reasons cannot be made public because the matter involves advice from the National Security Committee and its work must be kept secret.
She said officials have "faithfully followed" the vetting mechanism established to disqualify people from public office and the law is clear regarding what types of behaviour are unacceptable.