Network Rail could face a £75m fine if its performance does not improve, according to the rail regulator.
The Office of Rail Regulation (ORR) said that the rail authority had breached its licence in 2012-2013 as it had not "done all it should have to deliver punctual London Distance (LD) and London and South East (LSE) trains".
It warned that if the operator does not achieve its targets for LD services, a key commuter route, it could be substantially penalised.
The assessment also found that the rail operator's punctuality targets, which affected millions of passengers and 145,800 trains in the first financial quarter of 2013, were behind target.
"Network Rail must do what it has said it will do and use the funding it already has for further initiatives to close the performance gap and deliver its commitments," the ORR said.
The regulator revealed that the private company oversaw 7% more infrastructure incidents in Q1 2013 than the year before, causing an 11% increase in delays.
There were 11,925 infrastructure problems across the rail network in Q1 2013, amounting to a staggering 1,226,081 minutes of delays.
"Network Rail has been entrusted with large amounts of public and passengers' money, which, if invested well, should deliver the levels of efficiency and punctuality it promised to deliver," stressed ORR Chief Executive Richard Price.
"However, the company is falling short of expectations at the moment. It is facing many problems of its own making, having failed to deliver plans to renew Britain's rail network, with delayed works now affecting performance."
But the ORR did argue that the operator is generally on course to deliver its programme of enhancements to the rail network.
"Many projects will directly improve passengers' experience or help expand the Strategic Freight Network," said the ORR.
The warnings from the ORR follow the publication of two reports investigating Network Rail's performance and finances.
A spokesman for Network Rail said: "We have reduced the cost of running the rail network by almost 40% since 2004, but inevitably the pace has slowed as we carefully balance the needs of the business against stretching regulatory cost cutting targets.
"There is further headway we can make and have identified a further 18% of savings we believe possible by 2019."
He added: "Train performance is still, by historical standards, at a high level - last year was the third best year ever recorded - but we know we can do better, especially on our long-distance routes."
Norman Baker, the rail minister who is having meetings with senior Network Rail management figures this week, said: "I am, as I think the rest of the travelling public will be, dismayed to learn that Network Rail is still failing to tackle deterioration in the punctuality and reliability of the network - a matter I have regularly raised with them."