Man on the tracks at Flinders Street. Photo: Supplied

Police are negotiating with a man who has jumped onto train tracks at Flinders Street station, causing major delays across the rail network.

A police spokeswoman said police had been called shortly before 9.30pm and were still talking to the man nearly an hour later.  He was later arrested and taken to hospital for an assessment.

The incident caused major delays for nearly all metropolitan train lines while the city train station was shut down on police request.

Affected lines initially included Craigieburn, Cranbourne, Frankston, Hurstbridge, Pakenham, Sandringham, South Morang, Sunbury, Upfield, Werribee and Williamstown.

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Services have since returned to normal on the Cranbourne, Hurstbridge Pakenham, Sandringham and South Morang lines. Meanwhile, the delays had reduced for the Werribee, Frankston and Williamstown lines.

"Please listen for announcements, as trains will run direct to and from Flinders Street until further notice," Metro Trains posted.

The Metro Trains website was still warning commuters the delays on some lines were expected to last more than 30 minutes at about 10.30pm.