The iconic water fountain had only been running for three weeks after being out of action since February due to a failure of its pumping system earlier this year.

This most recent complication may have resulted from the jet's malfunction earlier this year.

The problem was discovered late on Thursday when a team of contractors was in the jet testing equipment and found the malfunction, National Capital Authority executive director Helen Badger said.

"We had attended to the repairs that we had with the irrigation problem we had earlier in the year and in addition to this process we were looking at doing some upgrade work while we were in there too," she said.

"The contractors were in in the jet when it was turned on and felt an unexpected vibration in the pump room."

The NCA shut down the jet and investigated so as to avoid further damage to the Canberra icon.

"It was a vibration that was enough to cause concern and obviously we don't want to damage the equipment more than it may be already, so we've taken the precaution of closing it for now," Ms Badger said.

Located in the central basin of Lake Burley Griffin in front of the National Capital Exhibition at Regatta Point, the jet was opened in 1970 to commemorate the bicentenary of Captain James Cook's discovery of the east coast of Australia.

The jet usually operates for two hours daily between 2pm and 4pm, sending water to a maximum height of 147 metres, and is a popular destination for tourists.

Ms Badger said the investigation would involve contractors testing all components of the jet, including its two pumps, but at this stage the NCA was unsure what had caused the problem.

"At this stage we're really not sure where the problem is," she said.

"But out of courtesy to the public we're letting people know the jet won't be running and we're hopeful that by late next week we'll have a better idea of what the issue is."