Some pillars at Tung Chung West Station were suspected of having concrete that did not reach the top.
MTR said a routine inspection found repair work that had not been approved. It instructed the main contractor to stop the work and submit a report.
The Highways Department said it received notification from MTR on Monday and sent staff to check the site. It has required MTR to submit a detailed investigation report within two weeks of notifying the department.
The department asked MTR to urge the contractor to carry out repairs promptly at its own expense, meet quality standards and avoid affecting project progress. The Tung Chung line extension is still expected to open in 2029.