Hundreds of Victorian babies have been diagnosed with the flu, prompting health authorities to warn pregnant mothers to check their vaccinations are up to date.

Key points: There have been 35,000 notified cases of the flu in Victoria this year, compared to 3,000 last year

There have been 35,000 notified cases of the flu in Victoria this year, compared to 3,000 last year Victoria's chief health officer is warning pregnant women to protect their unborn babies with the flu vaccination

Victoria's chief health officer is warning pregnant women to protect their unborn babies with the flu vaccination More than 340 babies have been hospitalised with the flu this season

Figures from Victoria's Health Department show there have been 416 reported cases of flu in children under the age of 12 months so far this year, compared to just 29 last year.

Victoria's chief health officer, Brett Sutton, said there were about 2,000 flu cases reported every week in Victoria, and there had been a spike in the number of cases in infants.

More than 340 babies have been hospitalised with the flu this season, and nearly 500 adults have also needed hospital care.

Dr Sutton said he expected at least some of the parents of the sick children had not been vaccinated.

"A number of them, I imagine their parents haven't been immunised because there's still only a minority of women who get the flu jab during pregnancy, but some of them as well will have developed flu even though mum's been immunised — that happens," he said.

Children aged between six months and five years are eligible for a free vaccination.

Dr Sutton said serious illness in babies too young for the flu jab could be avoided if a mother was vaccinated while she was pregnant.

"They're not perfect vaccines, but they can be given in pregnancy and they provide significant protection for unborn children," he said.

"It reduces their risk of developing severe disease and reduces their risk of hospitalisation, so it's a really important thing for any pregnant mum to consider.

"Flu always leads to hospitalisation for a small number of children, particularly young children [who] are vulnerable and some of them will end up very unwell.

"Vaccination is certainly important. Vaccination in pregnancy is safe and effective."

'We're probably in the peak of the season'

There have been 35,000 notified cases of influenza in Victoria this year, but the true number of people who have contracted the virus was likely many times that, Dr Sutton explained.

At this time last year there were fewer than 3,000 reported cases.

There were 5,000 at the same point in 2017, which was considered a bad flu year.

"We can't know the exact numbers, because there are a number of children who won't get tested, but in the middle of a big season there'll be a lot of children affected of course," Dr Sutton said.

"There'll maybe only be 10 per cent who actually get tested for the flu that get notified to the department. The true figure in every season is really 10s, to 100s of thousands of cases.

"It's probably peaking six weeks, two months earlier than it normally does, so we're probably in the peak of the season right now."

There have been more than two million flu vaccinations administered in Victoria this year, and 171 aged care residents have been hospitalised due to the virus.