Officials have approved just one in 10 - 23 of those applications - while 136 are still "in progress" or have been cancelled by the applicant.
Among around 70 to be declined is that of Roshni Sami's husband, who is stuck in the US, while she's alone in New Zealand seven-and-a-half months pregnant and "panicking".
"Its just awful. It's awful. It's stressful. It's consuming. It has a huge impact on me. I'm really worried about my stress levels and so are my doctors and midwife," she said.
"I think the first wake-up call for me was when I went to my 20-week scan alone. My mum and my close friend, who would sometimes come with me, were unable to come and I was on my own. My sonographer asked how things were going and I said - actually I'm really worried."
Driving to pick up a pram cover on Saturday, she said she was again reminded of why she shouldn't be alone in her third trimester when her car was hit by drunk driver.
She escaped uninjured but shaken, and spent a long night having scans to check their were no complications for the baby.
Another woman, Hannah*, said her partner needed to get to Australia and back after suffering a bad back injury.
He can't get the surgery in New Zealand, however she is expecting a child early next year and they're worried he won't get a spot in MIQ on his return.
"It's the unknown that's really so frustrating for us," she said.
"We wanted him to get this surgery done before the baby comes next year but there's no way to know when he could leave to go to Australia and then come back."
At the moment, there is no specific emergency allocation category for MIQ relating to pregnancy.
The Ministry of Business, Innovation and Employment (MBIE) said people could be eligible if they can prove they're travelling to provide critical care for a dependent person, and that no one else can provide that "critical care".
But meeting that criteria still doesn't guarantee a spot, it explained in a statement, because "it depends on the numbers of applicants and available places".
"These decisions are not easy ones to make and we are sympathetic to the distressing situations people applying for an emergency allocation are in. However, we need to balance each individual application with our critical work to ensure the safety of all New Zealanders and the limited available capacity in managed isolation facilities by sequencing beds as they become available.
"MIQ also needs to prioritise the applications to ensure they reflect the most urgent and time-critical situations."
Sami has launched a legal bid in the High Court to get last-minute emergency allocation granted for her husband.
She also wants better rights for others in the same situation.
Sami is in a Facebook chat with 13 pregnant women who have missed out on MIQ spots for either themselves or their partner, and all had their emergency applications rejected.
They're asking for pregnancy to be included in the emergency allocation criteria.
"Like most people I assumed there's an emergency system so if you do find difficulties, if you are in a critical situation, there's a remedy for that. What I discovered is that the remedy totally doesn't work... You're out on your own," she said.
Hannah said, 20 months into the pandemic, health authorities should have already done much more.
"It's just absolutely wrong to be telling these women they have to give birth without their support person."
In the meantime, clinical psychologist Jacqui Macguire said her advice for couples was to reach out to whatever support networks they can - and accept the situation, even if it isn't ideal.
"It's unfair. Nobody wants to be in this position ... thinking about MIQ and whether or not their partner can be with them," she said.
"We've just got to be in a place of acceptance. Frustration and stress is not good for you and it's not good for your baby."
The MBIE didn't respond when asked if it would consider reviewing the criteria.
It declined RNZ's request for an interview.
*Name changed for privacy.
