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Instead of 3100 rooms going online at 9am, officials cut capacity to 2050, citing a "rapidly evolving situation" with the new strain.
The rooms were available for dates between December and March.
An MIQ spokesperson said there needed to be enough room for international arrivals as well as community cases in coming days and weeks.
That included travellers from 'high risk' countries who needed to spend 14 days in the facilities, rather than seven.
The spokesperson said rooms would continue to be released in a safe, manageable way.
Some people who entered the booking lobby this morning have told RNZ they missed out.
Travel from nine southern African countries has now been banned to curb potential spread of the new Omicron coronavirus variant, after it was first identified in South Africa.
Institute of Environmental Science and Research principal scientist of genomics professor Mike Bunce previously said New Zealand was well placed to deal with the new threat but it was important to maintain border protections to "buy us time".