The hospital has played down the flooding, saying persistent rain caused some "minor leaks" and a partial drain blockage.

"The partial blockage has now been rectified and a minor leak was managed with no impact to service delivery," a spokeswoman said.

"Patients were not impacted. This was not connected to previous issues at the Centenary Hospital for Women and Children."

Images seen by The Canberra Times show flowing puddles of water covering parts of a corridor and makeshift barriers created to stop the flow of water.

The government has already had to undertake extensive work to rectify many issues at the hospital since it opened in 2012.

In 2018, 15 delivery suites and bathrooms had to be fixed due to water leaking into the wall cavities.

"Basically you've got soggy plasterboard and soggy vinyl floors," the executive director of infrastructure management and maintenance, Colm Mooney, said in 2018.

There have also been issues with the paediatric unit, part of which was closed for months due to plumbing issues.

Mr Mooney said those issues were caused by a pin hole in a pipe.

Opposition health spokeswoman Vicki Dunne said the government was trying to whitewash "serious" internal water damage.

"The Centenary Hospital for Women and Children has suffered a litany of structural failings even though the building is only eight years old," she said.

"The latest internal flooding raises series questions about what if any remedial work the government has done since these serious structural failings were first identified.

"It's hard to believe that this is the state of our hospital infrastructure when we are a wealthy jurisdiction, and the nation's capital.

"The ACT government is attempting to whitewash serious internal water damage at the Centenary Hospital for Women and Children."