A week after a 3-month-old boy was vaccinated against the rotavirus disease he almost died from an obstruction to his intestines - an issue known to be a rare response to the vaccine.

An immunisation expert said it was impossible to tell if the vaccine brought on the sickness. The family were told by doctors that Jude's case was as rare as one in 50,000.

But the family have spoken out to warn others to keep an eye out for symptoms and get treatment straight away if they became concerned.

"Ripped to shreds with stress," David and Sonya Cooper found themselves at Auckland's Starship children's hospital giving their baby boy one last kiss before he was wheeled away for urgent surgery at 4am.

Baby Jude made it through surgery two weeks ago but continues to be monitored.

The family's "week from hell" started two days after Jude received the rotavirus vaccine.

Rotavirus is a highly contagious virus that infects the intestine causing gastroenteritis and fever, predominantly in infants and young children.

Sonya said a day after Jude had the vaccine against the disease she noticed a clear change in him.

"He started refusing feeds, his nappies dried up and he was constantly grizzly, lethargic and spent his day flopped in pain in my arms."

The following day Jude deteriorated and started vomiting so Sonya took him to North Shore Hospital.

Jude was monitored for a couple of hours but doctors concluded he had a gastro bug and the family were sent home.

For three days Jude wasn't able to keep a feed down - he was struggling and so were his parents.

Then, Jude's condition took a shocking turn and he was sent to the emergency room at Starship.

Sonya said it was all go and the hardest thing was to stand back and watch as a group of strangers stepped in.

An immediate x-ray revealed an obstruction in Jude's intestines, confirmed by ultrasound.

"This is when we were informed that Jude's suffering was a result of the rotavirus vaccine. The live virus multiplied and spread hard and fast through Jude's tiny body," Sonya said.

The couple said they wanted to make it clear they are not anti-vaccinations but their experience has given them a new perspective.

David said obviously their case was the worst possible outcome and very rare but it happened.

"Just because the benefits outweigh the risks, doesn't mean we should forgo the communicating risks.

"In New Zealand we are fortunate to have a good health care available, so it shouldn't get to the point where we are told urgent surgery is the only option."

David said knowing risks would helped them to be more preventative before it got to that stage.

"If we had known more about the risks, we would have been more pushy the first time we saw the doctors instead of waving it off as a bad tummy bug."

Vaccinator Dr Helen Petousis-Harris from the Immunisation Advisory Centre (IMAC) said she was aware of the case but said it was impossible to know whether the rotavirus directly caused Jude's bowel obstruction.

"There are multiple triggers and it's very difficult to know. That baby could have had a tummy bug before getting the vaccination without anyone knowing."

Petousis-Harris said she agreed with the parents that the very slight increased risks should be communicated before the immunisation, with other risks to watch out for.

"There's nothing you can do that's absolute except to say there is a slight risk... but people need to consider the immunisation has prevented thousands of hospitalisations of gastro and intussusception [bowel obstruction]."

By the age of 3, nine out of 10 New Zealand children will have contracted rotavirus.

Death from rotavirus infection in New Zealand is rare, but prior to the introduction of the rotavirus vaccine in July 2014, 1 in 43 cases were hospitalised.

On the IMAC website it states the "common responses to the rotavirus immunisation injection are mild diarrhoea or vomiting and abdominal pain. Rare responses include intussusception.

"As with any medicine, very rarely, severe allergic reactions occur following immunisation," IMAC states.

"If there's one thing we've taken from this it's that the risks need to be better communicated. We would have been more ready if it was," said David.