In a regulatory filing last week, CA said that the investigation, being conducted jointly by the US Department of Justice (DOJ) and the US Securities and Exchange Commission (SEC), "appears to be focusing on issues relating to the company's historical revenue recognition policies and practices."
Parties outside CA have received subpoenas from the SEC in conjunction with the investigation, with which CA continues to co-operate voluntarily, the company said in its filing.
The federal inquiry concerns CA's restatement of earlier revenue as it relates to an infamous stock option award made in 1995, according to The Wall Street Journal.
That year, CA awarded a large stock incentive package to three top company officers, co-founders Charles Wang and Russell Artzt and then-president Sanjay Kumar, now also CA's chief executive officer.
The terms of the grant specified that the shares would vest when CA's shares hit and sustained a target price. The benchmark was met in 1998 and the three executives combined received nearly $1bn in CA stock.
But news of slowing sales soon dragged down CA's share price, and furious investors accused CA of manipulating its accounting to push the share price up to the grant's vesting price.
The executives later returned a portion of the shares from the grant to settle a shareholder lawsuit.
Investigators are examining why CA overstated revenue for a period surrounding the 1998 stock grant.
In May 2000, CA retroactively reclassified previous revenue and expenses for that period, a revision that investigators are probing, the newspaper said.
The 2000 change in expense and revenue classification came at the advice of its auditor, and had no material affect on CA's historical revenue growth patterns for the five-year period from 1996 to 2000, CA said in a statement.
CA's 1998 statements and financial projections remain the subject of a class-action lawsuit being pursued in a US District Court.
The case, a consolidation of several shareholder complaints filed in 1998, is now in the discovery phase following the court's rejection of CA's motion to dismiss.
In late 2000, CA again adjusted its accounting, radically changing the way it records sales revenue as part of a shift towards selling software through subscription licenses.
That change sparked another round of shareholder lawsuits in February and March of this year, after news broke of the SEC and DOJ inquiries.
Shares of CA were down 2.8%, at $17.07, in afternoon trading yesterday on the New York Stock Exchange.