The performance bonuses are reportedly worth millions of dollars to the rail operator every year.
The new system which uses track sensors at stations replaces the old practice where Metro staff were responsible for recording and submitting on-time and cancellation data to government.
The Public Transport Users Association's Tony Morton said the new figures confirmed a long-held view that Metro was skipping stations to meet punctuality targets.
"It is in fact confirming we have a system that depends on the systematic inconvenience of passengers," he said.
"The system ought to be running a lot better than it is and we can see the hard numbers now to see how well or poorly it is operating."
Metro said while there were "too many bypasses and cancellations" it denied altering services to make profits.
"When we have a disruption, we need to recover from that to returning the network to on-time running," spokeswoman Larisa Tait told 774 ABC Melbourne.
"So if we were unable to amend late-running services then those services would continue to run late all day."
Ms Tait said the documents had highlighted a particularly bad week for the rail operator.
The Victorian Government used the new figures to highlight the need for its planned Melbourne Metro rail tunnel.
Public Transport Minister Jacinta Allan said more investment was needed to boost the capacity of Melbourne's rail system.
"These figures are very frustrating for passengers who use the system every day and who are experiencing the inconvenience of having their service changed," she said.
abc.net.au 25 Mar 2015
More corporate fraud in the hand of multinationals.
The corporatised government literally supports corporate fraud, especially when it comes to defrauding the general populous.
Naturally no financial penalties apply, and even if they did they would be recuperated from the customers in terms of higher prices.
Another monumental fraud supported by the corrupt people in government.