The MTRC says there's a chance that a section of the roof at the West Kowloon express rail terminus may leak when the long-planned train service begins in September.
The MTR's operations director Adi Lau said on Tuesday that they spotted the leakage during heavy rain, but said it affects only "a minor area" of what is a big station.
Lau said workers will be doing what they can to rectify the issue. But if the leaks can't be completely fixed, workers will try to minimise the leakage area so that passenger areas won't be affected.
The MTR boss said he himself saw the leaks, but the problem hasn't affected the ongoing trial runs of the cross-border trains.
Lau remained vague about the number of high-speed services from the station when the line opens. He said the MTR is still working with its mainland counterparts on the matter.
It was initially proposed by a consultant that up to five trains a day should depart West Kowloon for long-haul destinations such as Beijing and Shanghai. But reports say this may be reduced to just one per day.