City Loop train services have resumed after a man was fatally hit by a train near Flagstaff Station on Friday afternoon.

The incident closed the loop to some services, causing major delays on the Alamein, Belgrave, Lilydale and Glen Waverley lines as trains were forced to run direct from Flinders Street to Richmond.

A Metro Trains spokesman said a person was hit by a train about 2.30pm on Friday but said at 5.45pm all lines running on their normal routes.

Customers on the affected lines were initially advised to make their way to Flinders Street.