Passengers on the Altona Loop in Melbourne's west have also been inconvenienced by the time-saving technique, in which loop stations are skipped so that delayed trains can get back on schedule.

Loop bypassing forces passengers to switch trains to reach their destination, creating disruption and overcrowding at busy inner-city stations such as Flinders Street and Richmond.

Figures for the first three months of 2015 reveal loop-skipping by Metro has more than doubled in the past year and is at its equal-highest level since records started being kept in early 2013.

In all, 1247 services bypassed Melbourne's two rail loops between January and March this year, compared with 588 in January-March 2014, data released by Public Transport Victoria shows.

Source: Track Record 62, Public Transport Victoria

The figures for the City Loop amount to 1.7 per cent of services, or about 14 trains a day, and represent Metro's worst quarterly performance for loop bypasses in two years. About 1.3 per cent of Altona Loop services were bypassed as well.

The 1247 bypasses included 1144 trains that skipped the City Loop and 103 that skipped the Altona Loop.

Jennifer Williams, a regular Altona loop commuter, said Metro bypassed the three stations on the Altona Loop as soon as there was "a sniff of a delay" on the adjoining and much busier Werribee line.

"Part of the problem is we never know when it's going to happen," Ms Williams said. "You go to the station and you can wait 20 minutes for a train, or it might be 40 minutes."

The sharp jump in loop bypasses also corresponds with a significant drop-off by Metro in station skipping, in response to a backlash by commuters and pressure from the state government.

Station skipping has infuriated commuters, who have been stranded on station platforms while Metro scrambles to get the trains back on time.

The operator has come under heavy political pressure to rein in the practice. Public Transport Victoria began publishing monthly figures for station skipping earlier this year.

Those figures show station skipping happened just 270 times from January to March, well down from last year when it occurred as often as 300 times a month.

But the sharp jump in loop-skipping this year has effectively cancelled out most of that improvement, with Metro simply using a different form of station-skipping to keep its trains on time.

Metro spokeswoman Pauline O'Connor said the company generally bypassed the City Loop because of congestion that caused trains to back up in the tunnels.

"Therefore, to avoid creating further congestion and knock-on delays, a service may bypass the Loop," Ms O'Connor said. "We try to do this as little as possible and only to assist with late-running services and avoid further delays."

The high number of bypasses in the first three months of this year were caused by a range of factors, she said.

These included heat-related speed restrictions in January, track faults and signal failures, ill passengers and trespassers in the Loop and even White Night, the all-night arts event in February.

Tony Morton, the president of the Public Transport Users Association, said Metro's franchise agreement with the state penalised the operator for loop bypasses, unlike station skipping which does not feature in the contract.

But he said the practice was still highly inconvenient to passengers and was in many cases another symptom of the long-term neglect of the rail system.

"Ultimately passengers don't care about the minutiae of the contract and arcane calculus of penalties and bonuses - they want the trains to run on time and where it's said they will be provided," Dr Morton said.