Metro boss Andrew Lezala says the company hopes it is in Melbourne to stay and will gladly meet tougher punctuality targets if that is what it takes to hold on to the contract to operate the city's trains.

But the man who runs Melbourne's railways warns the system may never function as smoothly as the public would hope, and he will not guarantee that Metro will ever fully stamp out station skipping or running short services to make up lost time.

"We're happy to accept a tougher target, definitely - we expect it," Mr Lezala said in an interview with The Age, although he declined to nominate a figure.

"We know that will be required and we're ready to accept it, but we've got to be realistic when we look at managing disruptions because there will always be constraints."

Metro has been accused of altering services to win multimillion-dollar government bonuses, an accusation Mr Lezala insists is a "misconception".

Metro's chief executive said the company altered train services only to get the system back on time as quickly as possible and minimise the number of people who were delayed, but he acknowledged that the public hated it.

The Age revealed last month that Metro shortened 550 services in a week.

"I realise that [Metro's] reputation is damaged through this practice," he said.

But he pointed to figures that showed that in the six years since Metro replaced Connex, Melbourne's trains had become much more reliable.

As this Metro graph shows, punctuality sat below 85 per cent by the end of 2009, months after Metro had taken over, and is now edging towards 94 per cent. It has not dropped below the 87 per cent threshold at which Metro is penalised for poor performance since early 2012.

Metro's eight-year contract to operate Melbourne's rail network expires in 2017 and Mr Lezala is determined that when it does the company will not be banished from inside the city walls like its predecessor Connex was.

It has its own punctuality target of 95 per cent, a figure that is well short of the 99 per cent of trains its Hong Kong parent company MTR runs on time in that city, a record that has earned it the title of the world's most envied railway.

In its present condition, Melbourne's rail network could aspire to such near perfection, Mr Lezala said, because most train delays were outside Metro's control.

Police interventions, ill passengers, trespassers, vandals and people being hit by trains disrupt about 3½ per cent of services a month on average, Metro says. Other delays are attributable to Metro's operational failure - faults with signals, trains or tracks, driver errors and shortages.

"With today's situation we could never get more than 96.5 if we were perfect, because of those things, and I'm afraid ill passengers will only have a bigger impact as trains get more crowded," Mr Lezala said.

Melbourne's trains are about as punctual today as they were 10 years ago, as this Metro graph shows. But about 100 million more passengers use the system each year.

Mr Lezala said passenger growth in the years ahead would place further strain on the system. The company was looking at employing more staff at stations to manage crowds, and was considering handing out food in the morning to stop people fainting on overcrowded peak-hour trains.

"We're trying to work out ways we can give people energy bars in the morning - if you've skipped breakfast, have one of these," he said.