The online booking system has been a focus of frustration for New Zealanders overseas struggling to return home and the off-the-cuff response left many upset.
Former television journalist Corinne Ambler described the message as "absolutely disgraceful" and suggested that the message's author should "look for a new job".
Others accused MBIE of mocking Kiwis' frustration and suggested it was proof that MBIE "knows the system is broken" before the tweet was deleted earlier today.
Joint Head of MIQ Megan Main told the Herald that their initial intention had been to "reduce stress" and apologised for causing upset.
"The current community outbreak means MIQ needs to carefully manage capacity as community members enter facilities to quarantine," Main said.
"We understand that it is stressful for people trying to secure a room when demand is high. We know that many people are constantly refreshing the website looking for rooms.
"The announcement about pausing the release and re-release of rooms was intended to reduce stress and inform people seeking to book a voucher, so that they could stop refreshing the website as there would be no rooms to secure.
"We apologise for not making this clearer in the tweet and for any upset caused."
Main added that the emergency allocation process remains open for Kiwis who require urgent travel within the next 14 days said the MBIE will let people know when the system returns to normal.
MIQ hotel investigated as possible source of outbreak
An outbreak source investigation centred on Auckland's Crowne Plaza MIQ has so far failed to discover how the virus spread from the suspected "primary case" into the community, as officials try to track down two people.
Health officials are looking at an atrium thoroughfare inside the Crowne Plaza building as it was used by six people at the time the earliest-identified case in the outbreak was in the nearby hotel lobby.
Of those six, four had been tested and three had so far returned negative tests. The fourth person is in the process of getting one.
"There are two people still to be identified, which police are assisting with," the Ministry of Health said yesterday.
While the space between the MIQ and the thoroughfare was divided off, the ministry said there was still the possibility of air flow between the two spaces.
"It has been confirmed the case was indoors while a very small number of people walked in the open walkway, which is well ventilated."
So far, the source investigation has focused on the Crowne Plaza, where the infected traveller arrived on August 7, and the Jet Park Hotel quarantine facility, where they were transferred to after testing positive on August 8.
Yesterday, Covid-19 Response Minister Chris Hipkins said transmission from border staff into the community had been "almost ruled out as a possibility", as more than 400 staff across both facilities had returned negative tests.
