Incoming Chief Secretary Eric Chan and constitutional and mainland affairs minister Erick Tsang on Thursday tested positive for Covid after taking PCR tests.
The government said they last went to work on Monday and Wednesday, respectively, and are currently under isolation.
Chan, who's now the head of the Chief Executive's Office, has been under quarantine since Tuesday because his wife came down with the coronavirus earlier.
Tsang's wife, customs chief Louise Ho, has tested negative but she's now undergoing quarantine because she's listed by health officials as a close contact.
"The Constitutional and Mainland Affairs Bureau and the Chief Executive's Office will conduct thorough cleaning and disinfection at the offices concerned," the government said.
It added that Covid-19 tests will be arranged for relevant staff members in accordance with the advice from the Centre for Health Protection.