The branches in Wan Chai, Tsim Sha Tsui, Yau Ma Tei, Wong Tai Sin and Tseung Kwan O were closed, a media agency reported.
Only two stores, one on The Peak and the other at the airport, were open in Hong Kong.
The labour department has received enquiries from affected workers.
The owner and operator of the closed outlets, Perfect Combo, was recently taken to court for rent arrears amounting to $1.03 million.
The US-based global fast food chain first arrived in Hong Kong during the 1980s.
Burger King closed all its outlets in the 1990s till the return of a shop at the Hong Kong International Airport in 2003.