The Transport Management Centre said train passengers travelling in both directions on the T1 North Shore, T2 Inner West and Leppington, T3 Bankstown, T5 Cumberland and T8 Airport South Line should allow plenty of extra travel time.

Rail replacement buses are assisting with passenger movement, but people are being urged to expect delays, changes in the timetable and longer than normal travel time.

Just after 7am, a fatal motorcycle crash on the Western Distributor at Pyrmont closed three out of four city-bound lanes and one westbound lane on the Anzac Bridge, leading authorities to advise motorists to consider alternative routes or expect significant delays.

The crash occurred when a 29-year-old man riding a motorcycle east on the Anzac Bridge lost control and was struck by a truck travelling in the same direction.

Paramedics worked to save the motorcyclist, but he died at the scene. A police spokesman said the 40-year-old truck driver, who was uninjured, will undergo mandatory testing.

Officers were told the motorcycle may have collided with a vehicle, described as a white Holden Commodore utility, before he collided with the truck.

Police are appealing for the driver of this vehicle to come forward, and are appealing for any other witnesses, or anyone with dashcam vision that could assist the investigation, to also come forward.

Three of four citybound lanes were closed for just under two hours as the scene was examined, but all lanes were reopened by 9am. At that time the TMC said traffic was queued over four kilometres along Victoria Road and about eight kilometres on the City West Link.

Bus services through Pyrmont, Ultimo and Rozelle were experiencing up to 60-minute delays at 9am.

By 10.30am, traffic had cleared in the inner west, but a breakdown in the Harbour Tunnel had closed one city-bound lane, causing heavy traffic back to Neutral Bay. By 11am, traffic across the city had eased.

A TMC spokesman said trains were still operating on the affected train lines but at a reduced capacity.

The train service changes have been put down to wet weather and "a larger than expected number of staff off sick" according to a Sydney Trains tweet, while another statement said it was an "operational issue".

It was unclear whether the issue also was related to earlier signal equipment repairs at Town Hall Station, but the TMC spokesman said the issue was being investigated and would hopefully be resolved quickly.

Peak hour commuters have reported numerous trains being cancelled and trains being filled to capacity when they did arrive.

with Jenny Noyes