In all, 220 MSD staff stand to lose their jobs - around 2.3 per cent of the workforce.
Oranga Tamariki, the children's ministry, said it had already fired 19 frontline staff who were covered by the Government mandate which required health and education workers to get two doses of the vaccine by January 1.
Bill Searle, deputy lead for national Covid coordination and support, said another five staff had resigned, and one retired.
In addition, 70 workers had been moved into alternative roles which did not involve interacting with other people. Of that total, half were social workers and the other half were frontline workers, such as people who worked in youth residences.
The impact on Oranga Tamariki's services is not yet known. Its social workers have previously had very high caseloads - 31 children per social worker - but they has been dropping since 2017 and caseloads were now around 16 children per social worker.
Oranga Tamariki also has an internal policy - separate from the Government mandate - that all staff are vaccinated by March 1.
So far, one person had been fired under this policy, and two people had chosen to leave. Another 55 office workers had not been vaccinated and would be dealt with on a case-by-case basis.
In all, around 2.9 per cent of the ministry's 5000 staff were unvaccinated, compared with the national rate of 4.5 per cent.
Searle said Oranga Tamariki was reviewing its vaccine policy in light of the police/defence decision last month.
By allowing unvaccinated staff to work in non-contact roles, the children's ministry had shown more flexibility with its staff than other government departments.
Unvaccinated staff at the Ministry of Social Development have protested about the blanket policy for vaccination which requires staff to have the vaccine even if they are able to work from home and never come into contact with others.
Lynda Whitlow, who worked in an administrative role in Canterbury, said she had been working at home since August and was not required to have face-to-face contact.
Whitlow, who is unvaccinated, said MSD appeared to have a policy of termination or vaccination, with no other options considered.
Experts say the risks of adverse events from the vaccine were far outweighed by the risks of Covid-19 infection. But Whitlow said she was hesitant to get vaccinated because she had severe reactions to childhood vaccinations.
Prime Minister Jacinda Ardern has indicated that Government vaccine mandates - which cover health, education, corrections and others - will be scrapped when they are no longer needed. A deadline has not been set, but Ardern has said that the strictest Covid settings will be eased after the Omicron peak.