Services on Tseung Kwan O line have been delayed due to unstable signalling system at North Point station, the MTR said during morning peak hours on Friday.
Journey time between North Point and Po Lam or LOHAS Park stations will add an extra five to eight minutes.
Trains are running at between six to eight-minute intervals, the MTR said
Passengers are advised to take the Tsuen Wan or East Rail line for crossing the harbour.
The MTR said crowd control measures were put in place at affected stations, and will arrange empty trains to pick up passengers when necessary.
Nidhi Bablani was among hundreds waiting for a train at Tiu Keng Leng station.
She told RTHK that she was not happy with how the railway operator dealt with the disruption.
"They could have probably arranged some other buses or something to get us to North Point faster," she said.
"Otherwise, it's annoying to stand in a long queue like this and wait for the train."
She added that the disruption made her stressed out, as she was running "extremely late" for work.
Another passenger, Novi, said the disruption would not pose too big of an issue for her.
"I will be late, but it's okay. You know like again as I mentioned sometimes a glitch happens. Then you just have to deal with it," she said.
The MTR had offered a 50 percent fare discount earlier this month to compensate for the disruption in the Tseung Kwan O line back in May.
When asked whether the MTR should offer discounts to compensate for the incident, Novi said she does not think a discount will make much of a difference.
"I think having a look at the disruptions to make sure that they won't happen again is more meaningful than the discount," she added.