Industry sources say that the shake-up was precipitated by Connex South Central, a key London commuter service. It refused to pay compensation to travellers under its passengers' charter after cancelling hundreds of trains a day. Experts had suggested this could have cost the company pounds 2.5m.
Connex, instead, argued that industrial action by drivers caused it to implement an "emergency" timetable. Rail passengers hit by industrial action in June - which saw nearly 20 per cent of scheduled services cut - will be given three days of free travel as compensation. Analysts say this would cost Connex only pounds 300,000.
The franchising director, John O'Brien, who oversees the privatised rail companies, claimed that the offer of three days' free travel was "reasonable". He added: "Many passengers did not receive an acceptable level of service during the summer and were therefore entitled to receive some form of compensation."
However Mr O'Brien's office has recognised that many travellers using the line will not be compensated for the cancellations. At present, passengers on InterCity services can claim a percentage for late-running or cancelled trains. Great Western, which runs services from London to Bristol, offers up to 40 per cent of a ticket price for trains more than an hour late.
Mr O'Brien is aware that thousands of travellers with weekly tickets or daily returns will be left uncompensated by Connex. This would change under proposals under consideration by his officials.
The Connex deal affects more than 15,000 season ticket holders on Connex South Central's south London line, where an 11-day strike by train drivers led to the cancellation of more than 200 trains a day.
Officials said they had taken a hard line. "This has set the precedent for future disruption. Operators have to give season ticket holders extra days for the disruption they face."
Under the privatisation performance regime, the franchising director - who split up and sold off British Rail to the private sector - did actually pay Connex a pounds 32,000 "punctuality bonus" for the trains the company did run.
Rail pressure groups also highlighted that the franchising director had allowed Connex South Central to raise its fares by up to 5.3 per cent next year. "What the franchising director is giving with one hand he is taking with another. Passengers can get a few extra days' travel but they are also facing above-inflation fare rises."
Rufus Barnes, secretary of the London Rail Users' Consultative Committee, said that Connex had said passengers were unlikely to get any compensation under the passengers' charter if their performance improved over the year. "Inner London services suffered a great deal. We think that three days free travel for season ticket holders is fair," he added.