In a statement, the administration said one of the plots is lent by a private developer and is located near Ma Sik Road in Fanling.
The other site is on the Hong Kong Boundary Crossing Facilities Island of the Hong Kong-Zhuhai-Macau Bridge.
The sites, together with several other locations announced earlier, are expected to provide about 50,000 beds.
Meanwhile, speaking on a radio programme on Friday, development minister Michael Wong said construction of the facilities are now underway in Kai Tak, Yuen Long, Tsing Yi and other districts.
He said the facilities, funded by the SAR government, will be built by mainland construction teams using the modular method – which involves assembling prefabricated parts on site.
Meanwhile, the authorities said 11 hotels are now providing some 3,800 rooms for isolation purposes.
They added over 30 hotels are being converted into community isolation facilities.
Separately, the government said Chief Executive Carrie Lam had conducted a virtual meeting on Wednesday with more than 100 officials, telling them “a huge amount of manpower” is required to operate the facilities and perform other anti-epidemic tasks.
A statement said officials who spoke at the meeting said they would deploy their existing manpower, and “as applicable also recruit retired members of the civil service” to take part in the operations.