Steve Jobs, chief executive of Apple, was warned in 2001 about the accounting implications of backdating stock options for top executives at the company, Apple’s former chief financial officer said on Tuesday.

The statement by Fred Anderson, who on Tuesday agreed to pay $3.5m to settle backdating charges with the Securities and Exchange Commission, raises fresh questions about the role played by Mr Jobs in improper backdating at the company.

It came as the SEC said it would not take any action against Apple itself. The regulator on Tuesday said its decision was due in part to the company’s ”swift, extensive and extraordinary cooperation” in the government’s investigation. However, fraud charges were filed against Nancy Heinen, the company’s former general counsel.

Mr Anderson’s lawyers declined to say whether he had made similar accusations under oath or as part of the SEC’s investigation into backdating.

While Tuesday’s events appear to signal that the enforcement agencies do not have evidence to pursue an immediate case against Mr Jobs, his standing as the most prominent executive to be drawn into the options backdating scandal that has engulfed more than 200 US companies has guaranteed close scrutiny of his role.

Apple has said Mr Jobs did not benefit from backdated grants and implied he was not aware of their accounting implications.

The company refused to comment on Mr Anderson’s allegations.

The SEC alleged on Tuesday that Apple backdated two large options grants, a February 2001 grant backdated to January 17 of that year, and a December 2001 grant backdated to October.

The earlier dates enabled the company to under-report compensation expenses by about $40m and personally benefited Mr Anderson and other top executives.

In a statement circulated by his lawyers, Mr Anderson alleged that he had received assurances from Mr Jobs in late January 2001 that an options grant to several members of Apple’s top management team had been approved by Apple’s board on January 2. That was two weeks before the January 17 grant date specified in Apple’s company filings.

Mr Anderson “was told by Mr Jobs the board gave its prior approval and the board would verify it”, Mr Anderson’s lawyers alleged.

“Fred relied on these statements by Mr Jobs and from them concluded that the grant was being properly handled. It now appears that the board may not have given the necessary prior approval to the grants.”

Mr Anderson also said he “understood” Mr Jobs and Ms Heinen selected the grant date.

The justice department is still investigating options backdating at Apple.