The ministry is concerned for the safety of staff who have to go to work at the Government Complex where the online system is situated, said Thongchai Chasawath, chief of the Consular Afffairs Department.
The venue on Chaeng Watthana Road is currently occupied by anti-government protesters from the People's Democratic Reform Committee (PDRC).
As a result, the ministry has had to use a backup system, which has more limited capacity, Mr Thongchai said on Saturday.
The ministry will have to assess the situation before deciding when to reopen the main system, and will notify the public on Sunday, he said. People can get updates at www.consular.go.th.
Passport issuance has been one of the highest-profile casualties of weeks of PDRC-led protests intended to pressure the government by crippling public services.
The Foreign Ministry on Feb 9 opened a temporary office at the Queen Sirikit National Convention Centre (QSNCC) in an attempt to meet demand for passports.
The temporary office can provide services for up to 600 people a day, but backlogged applications number in the tens of thousands because of disruptions to the service at Chaeng Watthana.