The Victorian Government has revealed a boom gate safety issue which has caused the cancellation of hundreds of regional train services this week has existed for the past five years.

V/Line trains have been banned from running on Melbourne tracks, excluding the Ballarat and Geelong line, after a VLocity train failed to trigger boom gates at Dandenong last Friday.

It has resulted in thousands of passengers being forced to switch to Metro services in the city's outer suburbs.

Acting Public Transport Minister Luke Donnellan said he was now aware of similar incidents dating back to 2011, in which V-Line trains failed to trigger level crossing signals.

"We're furious and we need to get to the bottom of this and we will," he said.

"What's been identified in the report was incidents in 2011 and '12.

"It's disappointing that that was the trigger to take action and comprehensively nothing was done.

"As to which particular agencies or so forth didn't undertake their role, that's what we're working through currently."

News Corp reported that Metro deputy chief executive Michael Houghton wrote to V/Line chief executive Theo Taifalos last May, warning that boom gates had problems detecting trains on level crossing approaches.

According to the Herald Sun, a report by Metro's top engineer in February 2013 recommended short-term fixes to reduce the problem.

Metro Trains refused to confirm the reports.

Mr Donnellan said he had not seen the documents but it was incredibly fortunate there had not been a serious accident in the last five years.

"We're trialling some track circuit assisters to see whether they'll improve the issue with setting off the boom gates," he said.

"We've asked the agencies to get moving to get this fixed as soon as we can."

The withdrawal of the Bendigo, Seymour and Gippsland lines from suburban tracks comes days after V/Line identified a fault in its fleet of VLocity trains resulting in most services being replaced by buses.

Calls for upgrade to avoid future problems

The Victorian Greens called for the regional rail network to be upgraded in the wake of the widespread service disruptions.

Greens Leader Greg Barber said the Government needed to upgrade the 19th-century signalling system.

"This is a serious commuter service, that people use to commute from regional cities into Melbourne," he said.

"Our tourist trade and major events all depend on it, so although it's an expensive exercise to upgrade a signalling system that's been left for so long, the extra capacity it'll give us on the network makes it a real bargain."

The Opposition is calling on the Government to release all engineering reports and correspondence that warn about the problems with boom gate triggers.