A fight broke out at Tin Shui Wai station in the morning forcing its closure, and the obstruction of train doors on Kwun Tong, Tsuen Wan, Tseung Kwan O and Island lines have caused delays, the city’s rail operator said.

Trains also skipped Yuen Long station earlier because of protester disruption, while large queues are building at the interchanges of Kowloon Tong, North Point, Mong Kok and Yau Tong as the impact of the direct action takes its toll on the rush hour commute.

At Kowloon Tong station, hundreds of commuters have to line up along the stairs all the way onto the concourse as train services are delayed. MTR staff have suggested people try other means of transport. #HongKongProtests

Overcrowding measures have been put in place at Kowloon Tong, an interchange connecting the busy commercial hubs of Kowloon with northern parts of the city.

As of 9.30am, six MTR lines were affected by service delays or station closures.

Classes resumed at primary and secondary schools on Wednesday, with about 100 pupils in Kwun Tong marking their return by disrupting traffic at the junction of Hip Wo Street and Tsui Ping Road. Riot police have arrived on the scene.

Mask-wearing secondary students in their school uniforms marched from Kwun Tong MTR station to the intersection before the start of classes. Some blocked roads with bricks, rubbish bins and metal railings as they called for the government to meet all five demands of the protest movement.

It led to flashes of disputes as commuters got off the bus and tried to clear the road.

Activists had issued calls on social media for protesters to “paralyse the whole of Hong Kong” on Wednesday morning.

The first trains of the day on part of the East Rail line were delayed for staff to clear several objects off the track near Fanling, including a bicycle hanging from an overhead cable.

At Diamond Hill station, where carriage doors were not closing, more than 100 passengers were unable to board trains during the rush hour.

A 58-year-old clerk at an accountancy firm in Central, who gave her name as Ms Wong, said she would be more than an hour late for work because of the delays at Diamond Hill, and feared having to take the whole day off.

“I feel angry. I wanted to go to work, but there’s nothing I can do ... The [protesters] have affected our livelihood, bringing Hong Kong to a standstill,” Wong said.

Another commuter at Diamond Hill station was less put out by the disruption, saying her boss would understand why she was late.

Meanwhile, the Transport Department has put on free ferry services and diverted buses to cope with the ongoing closure of the Cross-Harbour Tunnel, which connects Kowloon with Hong Kong Island.

A statement issued by the government on Wednesday morning urged employers across the city to make flexible working arrangements for staff affected by transport disruption.

"The government will similarly handle government employees in such situations with understanding," it said.

Wednesday marked the return of classes at primary and secondary schools following suspensions over several days because of the transport chaos caused by protesters.

Many pupils arrived early after demonstrators said they would take direct action across swathes of the city, with several saying they were glad to be back in school.