Run by the bus company Stagecoach, SWT attracted criticism for cancelling up to 39 trains a day in February and March after making 70 drivers redundant.
The rail franchising director John O'Brien said yesterday he would not be fining the company but warned SWT that it faced "financial penalties and further serious sanctions" if cancellations increased again.
SWT runs services out of London's Waterloo station to suburbs and as far south-west as Weymouth and Exeter.
The company agreed a redundancy package with drivers at the beginning of the year, but then ran into difficulties when other drivers needed to go on route-familiarisation courses.
"Passengers on SWT suffered an unacceptable level of cancellations in February and March and my priority was to see services restored to normal," said Mr O'Brien.
He said he would have imposed the special pounds 1m fine if SWT had run less than 98.5 per cent of its services in April. But the company had run 99.6 per cent of trains - which Mr O'Brien described as a "significant improvement." But he warned that if cancellations rose again above 1.5 per cent he would threaten penalties.
The pounds 1m fine with which SWT was threatened was above the normal penalties which rail firms face for failing to meet monthly performance targets.
It had already been fined about pounds 1m for its poor record in February and March.
The Transport Minister, Gavin Strang, said yesterday. that he had asked for a report on "the shortcomings of the sanctions currently available to the regulators, to assist in our review of the railway".
He added: "The SWT episode supports our belief that the weapons available to the regulators are inadequate.
"Train operators across the country are on warning: this government will not tolerate inadequate performance."
The Save Our Railways group said it was disappointed at Mr O'Brien's decision. Its coordinator, Jonathan Bray, said: "The pounds 1m fine always was a gimmick. For a while the franchise director posed as a tough regulator - now he's reverted back to being weak and ineffectual."Reuse content