Workers and officials from the Unite union claimed there were only eight toilets for a total workforce of 650.
Site workers also said the loos were dirty and they have been forced to bring their own toilet paper in.
The row erupted at a new £300m multi-fuel facility at Ferrybridge near Castleford where Hitachi Zosen Inova is main contractor.
Union member Peter Beaumont told the BBC: “When you need to go to the toilet you don’t have time to start balloting the members.
“When you’ve got 100 men who need to clean their hands before dinner it’s quite an important thing.
“We needed to withdraw our labour.”
Workers returned to the site on Tuesday afternoon after management agreed to provide more toilet blocks and extra cleaners.
