Managed isolation is now booked out until November, although the government says more vouchers will be released to meet the high demand.
Room bookings at border hotels for December are likely to be available next month, including for New Zealanders returning for Christmas.
MIQ said further vouchers for upcoming months would be released, but explained that capacity in the system had been reduced by 900 rooms a day, out of an operational total of 4000.
More than 450 rooms are out of use because of maintenance work at the Grand Millennium and M Social hotels in Auckland. The Mercure hotel reopened at the weekend after work was completed on its ventilation systems.
While an estimated 1000 spaces had been freed up by the trans-Tasman bubble, another 500 contingency rooms had been set aside as a result of the quarantine-free travel launch.
"We are currently experiencing high demand for MIQ vouchers," Joint Head of MIQ Brigadier Rose King said.
"Vouchers for MIQ are gradually released in batches over several weeks and months to assist people in different time zones and to help manage the number of users on the site at any one time.
"There are still more rooms to be released for August, September and October. We advise people to keep checking the system for available dates.
"Vouchers for December will be released once airlines have confirmed their schedules. Airlines are likely to have schedules available in July 2021 for November onwards."
Cohorting - grouping guests together according to their arrival dates or arrival planes - was among the factors that had affected the number of rooms available.
"Recently, we have been operating at a lower capacity due to ongoing planned maintenance work, implementation of cohorting and both the Grand Mercure and Grand Millennium having been offline," she said.
"This means, MIQ has been operating at 3100 rooms per fortnight, down from our normal operating capacity of 4000."
Contingency rooms - 400 set aside for emergencies and unexpected peaks - have swelled to 900 since the introduction of the trans-Tasman bubble.
According to the MIQ website, that was designed to help "with the changing MIQ operating environment" as lower risk travellers from Australia are "replaced" by travellers from higher risk points of origin.
They also provide additional capacity in the event of some travellers needing to go into MIQ at very short notice (i.e. their plane is already in transit when a suspension is imposed).
The government noted earlier that it expected the bubble to free up 1000 to 1300 spaces.
Almost 150,000 people have been through managed isolation hotels since March last year and the voucher system was started last November to co-ordinate arrivals with border accommodation.
The ebb and flow of MIQ availability have affected many of those who have been through the system. Hundreds of managed isolation vouchers came free in April, after demand outstripped supply in the preceding six months and in particular during the run-up to Christmas.
But the booking system has faced criticism after website crashes when vouchers were released and because of the need to monitor websites or social media to find out when other rooms become available.
National last week spoke out about the cost and waste of unoccupied rooms, saying the government could use them to allow more critical workers into the country as well as to reunite split migrant families.
"At the moment there are on average over 1500 rooms vacant every day in MIQ, and over 9000 MIQ room vouchers have been unused since the beginning of the year," said its Covid-19 response spokesperson Chris Bishop.