Scanlon told the newspaper they were ready to disembark, but it was stuffy so they wound down their car windows.
Nearby, two Interislander workers were busy with some drums and pipes.
Then something went wrong, Scanlon said.
"There was a shower of liquid and an immediate odour."
Urine showered the driver's side of the car, and some of it came through the open windows and hit Scanlon and Jack.
"It was a 'wee' mistake," Scanlon joked.
"They were fiddling around with these blue drums, then we got a golden shower."
The workers were also drenched in the urine.
One was standing nearby "in white overalls looking absolutely horrified, totally drenched in pee".
The family attempted to clean their car with an old towel and wet-wipes, while Jack cleaned their clothes.
One of the workers tried to help, but the liquid was sticky and hard to remove, Scanlon told the Westport News.
The family had a smelly drive to Blenheim - a 25-minute journey - where they used a car wash and bought antiseptic spray to clean the inside of the car.
But it wasn't until they got to Westport - a further three hours' drive - that they could properly clean the car.
Scanlon said he was concerned for the welfare of the workers who were drenched in the urine.
"As a worker, it would be a pretty miserable thing to happen," he said.
"It's also not a very good look to be spraying passenger cars with human pee."
After immediately complaining to Interislander on Monday, a representative called them back on Friday.
They said the worker who was doused in the urine was taken to hospital to be checked and was okay, Scanlon tweeted.
Interislander promised not to clear the toilet tanks while people are on deck, apologised to Scanlon and offered him a refund.
Interislander executive general manager Walter Rushbrook told Westport News it was an "unfortunate incident".
"Interislander staff were working to clear a blockage in the sewage system which turned out to be caused by a pair of underpants flushed down an onboard toilet.
"The ferry's toilets are a vacuum pressure system, and we have signage to advise that only the toilet paper supplied can be flushed down.
"We only have a relatively short amount of time between sailings to load and unload the ships plus attend to urgent maintenance issues, which is why we were trying to the trace the blockage issue at the time the ship was discharging vehicles.
"Toilets get blocked from time to time and our staff are used to managing them.
"Our maintenance staff wear standard protective gear and have preventative immunisation shots. As with all incidents that occur, we will review our processes and procedures.
"We are investigating why the calls were not escalated."
