The system will be reactivated at 10am on Monday. It has the capacity to produce 6,000 passports a day, director-general of the Consular Affairs Department Thongchai Chasawath said.
"Those 4,000 people who did not receive service last Friday will be served first, so there will be only 2,000 spots left for other people. I am asking those who have no urgent need to use a passport in the next 20 days to visit on other days in order to alleviate a long queue tomorrow (Monday)," he said.
The department abruptly closed the system on Friday due to concerns over the safety of staff who had to go to work at the office near the Government Complex.
Protesters led by Phra Buddha Issara of the People's Democratic Reform Committee (PDRC) have occupied the area on Chaeng Watthana Road in front of the complex.
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 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.