Tempers flared as commuters complained of being stranded on Monday morning as the network ground to a halt.

One Age reader said his journey from Cranbourne to Melbourne Central took 2 hours and 40 minutes.

Many others complained of being trapped on stationary trains for up to an hour.

Boom gates on the fritz in both Alphington and Clayton added to long delays, causing traffic jams for motorists and plunging bus lines into turmoil.

Metro spokesman Marcus Williams said lots of little faults occurring around the same time had compounded delays.

He confirmed one train on the Cranbourne Pakenham corridor was 80 minutes late.

"There wasn't anything connecting them all, unfortunately it was multiple issues in the morning peak.

That has knock-on effects."

"If a train is coming into the city, it might be going on to another service on another line. If that service is delayed, that's why there's delays on another line."

The Frankston line was the first to fall, about 6am, after a track equipment fault at Carrum sparked delays of 30 minutes.

Shortly thereafter, passengers on the Werribee line found themselves stranded due to a faulty train.

By 7am, the Cranbourne and Pakenham lines had delays of up to 20 minutes due to a signal fault in the Huntingdale area.

Services on the Frankston line were soon cancelled, while a faulty train stopped a Lilydale service to Flinders Street dead in its tracks.

A signal fault at Bonbeach plunged the Frankston line into further turmoil while a faulty boom gate in Oakleigh put local buses up to 40 minutes behind schedule.

The Hurstbridge line fell over shortly after, with a track equipment fault near Clifton Hill causing delays of up to 20 minutes.

Mr Williams said boom gates automatically come down when trains are in the area.

Due to equipment faults and a backlog of trains in some areas, boom gates were stuck down for extended periods throughout the morning.

Passengers complained of being stuck on trains for more than an hour and have threatened to take Ubers home instead, calling them more reliable.

An issue at Flagstaff Station also had trains on several lines skipping the city loop altogether.

Wrote one commuter on Twitter: "2.5 hours on the train and I'm still not at work, what a Monday".

2 hours so far to get to work. Still at least 30min to go. Usually an hour. Does @metrotrains offer compensation for lost productivity???? David Lamb (@davenlamb) May 28, 2017

The delays saw many people arriving to work several hours late.

One Twitter user said she arrived at Flinders Street Station at 10.17am - 90 minutes after her planned arrival of 8.44am.

One student told Fairfax Media they risked missing an exam because of delays on the Metro Train network.

"A lot of university students are having exams coming up this week or next week and many of us need to get to university to study or talk to tutors/lecturers before they commence," they wrote.

"However, the constant delays that plague this train system has cost many of us the chance to do so."

By 11am, Metro Trains was still working to ease delays, running trains directly to Flinders Street and skipping the city loop.

Mr Williams said the delays would clear around midday and said Metro Trains was not anticipating any delays during Monday afternoon's commute home.

@pauld08 @metrotrains @DanielAndrewsMP Your doing better than me. 2hrs 15mins to Caulfield. Would have been quicker walking??? Alex Burton (@alexanderb) May 28, 2017

@metrotrains 2 hours and counting. Left Pakenham 740am. At 940am we just got to Clayton station.
Supposed to be at Flinders at 843am!??? missjodielou (@miss_jodielou) May 28, 2017

@metrotrains @JacintaAllanMP 150mins to go berwick to sandown park back to Dandenong. Still you say 60min delays??? jeff watkins (@jeffw0303) May 28, 2017

@davenlamb @metrotrains Weve been stopped an hour and I could have walked to dandenong and back 12 times over. I srsly wanna get off and walk pic.twitter.com/Jh4TKp61g8??? Sapphire Smith (@SappireSmith195) May 28, 2017