A spokesman for the airport operator confirmed the plumbing problem to AFP and said that by mid-afternoon on Friday, 51 out of 144 toilet areas were still affected.
The problem was caused by electrical issues with pumps supplying water to the facilities, the spokesman for Japan Airport Terminal said on condition of anonymity.
"We were notified by staff around 5:00 a.m. (2000 GMT Thursday)," the spokesman said, adding that the problem took 11 hours to resolve."
Running water was available at sinks, where people wash their hands, but not at many toilets," he said.
"Our staff directed our guests to functioning toilets. In some cases, our staff used buckets to wash toilets after use."
Passengers expressed panic on social media.
"I'm glad I made it to Haneda safely... but I can't use the toilet. This is an emergency," one user wrote on X."
Most toilets in Terminal 2 are out of order... As someone with a sensitive stomach, this is a pain," said another.
A third person said there were long queues for the toilet at the airport's train station, describing "utter chaos at Haneda Terminal 2".