Train services between Mong Kok East and Tai Wai on the East Rail Line were suspended on Sunday afternoon because of a person on the track at Kowloon Tong.
The MTR said free shuttle buses were operating between Kowloon Tong and Tai Wai.
The rail company said journeys on other parts of the East Rail Line could take longer than normal.
By 1.40pm, services were said to be getting back to normal.