The statement was made after a staff member from a clinic at Hanoi's Doi Can ward was reported to offer vaccination services at home for children at high costs earlier this week.
Tran Dac Phu, head of the ministry's preventive medicine department, said the ministry had warned staff not to vaccinate children in their homes.
Parents have also been encouraged to take children to hospitals and clinics for their safety, he said.
It had been announced that hospitals and clinics would be short of the imported 6-in-1 vaccine, which protects children from diphtheria, pertussis (whooping cough), tetanus, polio, Haemophilus influenza type B (HiB) and Hepatitis B, until next year. However health staff reportedly offered the vaccination at home, at the cost of VND3 million (US$130), three times higher than the normal price.
Other vaccines were also offered, priced between VND100,000-150,000 (US$4.4-6.6) above their normal cost.
Nguyen Thu Trang, mother of twin girls in Hanoi's Thai Ha street said she had used the service for her children since they were born six years ago.
"It's convenient and saves my time. The health staff reminded me of the vaccination schedules. We don't have to travel around or wait for our turn," she said.
However, Trang said, the health staff did not mention the oral vaccine of Rotavirus, so the girls had issues with diarrhoea.
Phu said the staff's behaviour was not endorsed by the ward's health clinic.
"The home vaccination service has long been banned as any type of vaccination can cause anaphylactic shock," he said, "which is dangerous without immediate treatment".
Nguyen Nhat Cam, director of the Hanoi preventive medicine centre said that only licensed hospitals and clinics could meet the strict requirements on storage, check-ups before injection, injection techniques and after vaccination care.
Cam asked people to report anyone offering home vaccinations to the centre's hotline on 04.39985765. He said anyone caught would face strict penalties or dismissal.