Upgrading signaling systems could cause more delays this year, the MTRCL warned as it announced a record number of 1.76 billion passengers last year.
The rail operator is upgrading the signaling systems of eight lines, which will help increase the frequency of trains.
Tests will be conducted after rail services stop at night and before they resume in the morning.
Staff will have to switch to a new system for testing at night and switch back to the old system in the morning.
Tests on the Tsuen Wan line will start later this month, while those for the East Rail line will begin in March.
New signaling equipment will be installed on the Island line, while the Kwun Tong line will get an upgraded equipment room.
"From local and overseas experience, we can say that a systems upgrade poses risks on service performance," operations director Adi Lau Tin-shing said. "But we have to make a balance and minimize the impact."
The number of incidents arising from the installation of signaling equipment may increase, he admitted, but the risk is manageable.
He advised passengers to check rail updates before they travel to work or school.
Lau said the increasing number of passengers and expansion of rail networks has been a major challenge for the MTRCL.
More than 1.76 billion passengers traveled on heavy-traffic rail routes - excluding the Light Rail - last year, a record high since the MTR and KCR merged in 2008.
The Kwun Tong Line Extension and South Island Line, which launched in October and December 2016, see about 110,000 passengers a day.
There were 10 serious incidents causing service delays of more than half an hour last year, an increase of two from 2016.
Last month, tens of thousands of commuters were stranded on the East Rail line when a signaling fault halted 14 trains.
Lau again apologized to affected passengers yesterday, saying an investigation will finish by March.
In 2017, MTRCL spent more than HK$8 billion on maintenance and upgrade, he said. The company also hired more operating and maintenance staff, with their number exceeding 12,000 last year, up from around 10,000 in 2013.