The Interislander ferry service has apologised after a family heading across the Cook Strait had their vehicle covered in human urine this week.

Sean Scanlon and his family were heading home from the North Island on Monday when they suffered what he describes as a "wee mistake".

He told the Westport News that two workers, who also became soaked, were doing maintenance on some pipes and drums when the incident happened.

"They were fiddling around with these blue drums, then we got a golden shower," Scanlon told Westport News.

"There was a shower of liquid and an immediate odour."

He said urine ended up on his family's car and some made it in through the windows.

"It would be good to know they had a process where they don't park people's cars next to things that can go wrong," he told the newspaper.

Interislander executive general manager Walter Rushbrook told Newshub it was an "unfortunate incident", adding they've been in contact with the Scanlon family to apologise.

Staff were working to clear a blaockage in the sewage system caused by someone flushing a pair of underpants down one of the toilets, he said.

"As part of tracing the fault, there was an unusually high pressure build-up which resulted in waste leaking at one location on the vehicle deck, adjacent to the family's vehicle," said Rushbrook.

"Toilets get blocked from time to time and our staff are used to managing them.

"As with all incidents that occur, we will review our processes and procedures."