The leaking toilet was discovered when astronauts pulled up floor panels onboard the capsule ahead of Sunday’s return.
The problem on the SpaceX capsule was first discovered during September’s private flight when a tube came loose and urine leaked beneath the floor.
NASA says that the astronaut will wear absorbent “undergarments” rather than have access to the broken toilet during the 20-hour ride home.
American astronaut Megan McArthur said on Friday that the situation is “suboptimal” but that the crew will cope with the inconvenience.
“Spaceflight is full of lots of little challenges. This is just one more that we’ll encounter and take care of in our mission. So we’re not too worried about it,” she said during a briefing from space.
Ms McArthur and her fellow astronauts have been at the ISS for six months.
NASA bosses have decided to bring them home despite the launch of their replacements being delayed due to weather and a medical issue with one crew member.
SpaceX is aiming to launch the replacement crew into orbit on Wednesday.
Ms McArthur will be accompanied on the trip home by NASA astronaut Shane Kimbrough, French astronaut Thomas Pesquet, and Japanese astronaut Akihiko Hoshides.
Two Russian astronauts and one American will remain onboard the ISS.
During the mission, astronauts grew the first chili peppers in space, which Ms McArthur described as “a nice moral boost”.
“They have a nice spiciness to them, a little bit of a lingering burn. Some found that more troublesome than others,” she added.
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