President George W Bush requested and received funding of $400 million (£200 million) for the plan after he made a secret appeal to Congressional leaders last year.
The money is likely to be used for operations carried out by the CIA and other intelligence agencies, according to the New Yorker magazine.
The appeal for funds “was focused on undermining Iran’s nuclear ambitions and trying to undermine the government through regime change” said the magazine.
A source cited the contents of the appeal – known as a Presidential Finding – as involving “working with opposition groups and passing money”.
The magazine claimed that American special forces had been conducting cross-border operations into Iran from southern Iraq since last year.
This was denied yesterday by Ryan Crocker, the US ambassador to Iraq.
“I’ll tell you flatly that US forces are not operating across the Iraqi border into Iran, in the south or anywhere else,” he told CNN television.