Managed isolation hotels released 2434 people yesterday, after the duration of stays was halved for international travellers.
Returnees now stay for seven days, then do three days isolation at home.
MIQ officials said 2533 people were already eligible to leave when the new rule came into force yesterday, having been in MIQ for seven days or more.
That meant about eight times the number of people exiting the hotels at once compared to a typical day, and each had to have a health check and low risk indicator completed.
MIQ officials had warned that it might take more than one day to process all the departures - and say 99 people were approved to stay another night.
In a statement, joint head of MIQ Brigadier Rose King said it was "a really big day for the staff" in the facilities.
"It was among the biggest changes we have put into place since MIQ began," she said.
"I want to thank all those returnees who departed yesterday for their patience and cooperation. I also want to thank MIQ staff for their extraordinary effort."
MIQ officials said there would be more rooms available for international travellers "thought not substantially initially."
Further details on how many will be released - as MIQ vouchers - are expected shortly.