Passengers were stranded in the City Loop after a man ventured onto the tracks near Melbourne Central station on Thursday morning.
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The incident, which prompted authorities to shut down the Loop, occurred about 9.30am.
All lines across the network were delayed, except for the Stony Point line.
Stranded passengers reported that their trains stopped, or were moving extremely slowly through the Loop.
Some passengers were stranded for more than 20 minutes.
A spokeswoman for Metro Trains said police had asked for trains in the Loop to be stopped, while they dealt with the situation.
Shortly before 10am, Metro's website said trains services had resumed, with delays of up to 15 minutes.
All lines delayed due to a trespasser in the Loop (except for Stony Point, finally a good service!) @metrotrains pic.twitter.com/56RbYUb4Wk— Tom Cowie (@tom_cowie) November 25, 2015
Support is available for anyone who may be distressed by phoning Lifeline 13 11 14; Mensline 1300 789 978; Kids Helpline 1800 551 800.