A pair of reports published Wednesday suggest Apple Computer is in deeper legal trouble than previously thought over stock option backdating. The company itself may shed more light on its stock options backdating involvement on Friday, when it is scheduled to file its annual report.

According to The Recorder, federal prosecutors are looking into whether company officials falsified stock option administration documents in order to maximize the profitability of option grants to executives, citing people with knowledge of Apple’s situation.

Citing anonymous sources with knowledge of the case, the legal publication reported that allegedly faked documents were uncovered in a three-month internal probe conducted by Quinn Emanuel Urquhart Oliver & Hedges that concluded in October.

On October 4, a regulatory filing by Apple said that investigation “raised serious concerns regarding the actions of two former officers in connection with the accounting, recording and reporting of stock option grants.”

In the same filing, Apple announced that Fred Anderson, Apple’s former CFO, had resigned from its board of directors. The company noted that Anderson, who served as CFO from 1996 until 2004, informed the company that he believed his resignation was in Apple’s best interest.

According to The Recorder, which cited unnamed sources, the two “former officers” referred to by Apple in October are Anderson and former general counsel Nancy Heinen.

The publication noted that Heinen left the company last spring before the options scandal blew up. The publication said that Heinen lawyers Cristina Arguedas and Miles Ehrlich declined to comment.

It also said that Anderson’s lawyer, Jerome Roth of Munger, Tolles & Olson, declined to comment on his client’s situation.

In the other report Wednesday, the Financial Times said Apple CEO Steve Jobs was handed 7.5 million stock options in 2001 without the required authorization from the company’s board of directors, citing people familiar with the matter.

Records that supposedly showed a full board meeting had taken place to approve Jobs’ compensation, as required by Apple’s procedures, allegedly were falsified.

The FT said the SEC is now reviewing these and other pieces of evidence as it mulls whether to pursue a case against the company or any individuals over the options affair. The paper said an Apple spokesman refused to comment on the matter, but said the company had handed over the findings of its internal inquiry to the SEC.