The comments were published alongside the ORR's national rail review paper, highlighting the large quantity of work that needs to be completed over Christmas and New Year.
ORR chief executive Bill Emery said: "Engineering work on the railways is vital in order to maintain the network and to bring about the improvements to capacity, performance and safety that rail travellers expect.
"But Network Rail knows it is required to reduce the amount of disruption caused by its engineering projects, and avoid the sort of overruns we saw last year.
"Passengers and freight users alike will shortly be able to see the improvements brought about by the long-running work on the west coast main line.
"By finishing this work to the latest agreed plan, Network Rail will show that it has responded positively to the challenges posed by this programme. It can further help re-establish public confidence in its work by completing its Christmas engineering plans on time," he said.
Despite this warning, the latest set of figures from ORR's national rail review shows record performance on the network.
For 22 June to 13 September 2008, the public performance measure (PPM) for performance and delay minutes was at 90.5%, slightly above the target of 90.1%. Delay minutes are 9.8% down on the same period last year, at 3.84M delay minutes.
The regulator said infrastructure reliability is still improving, with the performance of track assets showing the most notable improvement. Assets are failing less frequently, and the overall level of delays caused by infrastructure continues to fall. Safety remains at an all-time low, and Network Rail is outperforming its budget.