News of the SEC probe, being conducted jointly with the US Attorney's Office for the Eastern District of New York, first spread in February when CA confirmed press reports of the inquiry. The investigation "appears generally to be focusing on issues relating to the company's historical revenue recognition policies and practices," CA said.
CA reorganised its business model in late 2000, shifting its sales focus to selling software on a subscription basis and altering its accounting to recognise revenue from sales throughout the life of contracts, rather than all at once when they are signed.
While CA maintains the accounting change was made to increase the clarity of its financial reporting and steady its revenue, charges that the move was intended to mask slumping sales have dogged the company.
A formal SEC order of investigation gives the organisation's staff authority to issue subpoenas and take testimony, CA said, stressing that the order does not reflect any determination of guilt.
CA's accounting is also at issue in several shareholder lawsuits seeking class-action status, filed in February and March. CA said it remains confident that the facts do not support the charges.
The SEC filing comes one day after CA reported a $238m (£163.3m) net loss for its fourth quarter, on revenue of $772m.
Shares of CA were down 4% in afternoon trading on the New York Stock Exchange, at $18.29.