The company, which was forced to cut hundreds of trains earlier this year, said that it had inherited a "high occurrence of annual leave over the period" and drivers were returning to work.
SWT, which runs services from London's Waterloo station to Berkshire, Surrey and Hampshire, was the first British Rail train company to be sold to the private sector.
Its new owners, bus giant Stagecoach, did little to endear themselves to the paying public however when management sacked too many drivers, causing services to be cut without warning.
The franchising director, who oversees passenger services, also threatened to remove Stagecoach's licence.
The company is determined to head off another shortage this summer - and implemented a bonus scheme.
Train crews are being offered cash bonuses of pounds 250 a day and up to pounds 1,500 to give up a week's holiday and work instead. The scheme has been called into question by the Health and Safety Executive.
The HSE warned that it could take action against SWT if any breaches of safety law were found in the scheme. Drivers can work 13 consecutive days in any two-week period under the safety rules.
But SWT said nothing it was proposing was against the law and it also dismissed claims by a rail pressure group that what it was doing was wrong.
The HSE said it had asked SWT for details of its plan and added that, under 1994 regulations, staff doing critical safety work could only operate for a limited number of hours.
"If we find any breaches of safety laws, legal action could be taken," said the HSE.
SWT said: "We are not breaching any regulations. Nobody will be allowed to work any longer than is permitted."
A spokeswoman added: "We restructured drivers' arrangements earlier this year, but are honouring holidays in the old roster system.
"We have taken a short-term measure to offer a bonus scheme to cover this holiday abnormality over the next few weeks."
But Keith Bill, the national secretary of pressure group Save Our Railways, said: "This is another management foul-up and taxpayers are having to fork out.
"The scramble for increased profits has to led to this problem, which is down to a huge management mistake."Reuse content