The Securities and Exchange Commission and Justice Department appeal followed Wall Street Journal reports that an internal security team at the retail giant secretly investigated employees and critics, including shareholders it thought might challenge company policies at an annual meeting.
Wal-Mart did not immediately respond to a United Press International request for comment.
In a letter to U.S. Deputy Attorney General Paul McNulty, Thompson blasted the reported activities as "chilling and truly outrageous."
The Bentonville, Ark., retailer's reported conduct "reflects breathtakingly flawed judgment and raises significant questions regarding Wal-Mart's commitment to its shareholders and the public markets," Thompson said in a letter to SEC Chairman Christopher Cox.
In all three letters, Thompson characterized as "troubling" Wal-Mart's assertion that it considered "this conduct to be justifiable and proper" and that it would "continue to conduct these activities in the future."
The New York City Pension Funds, which the comptroller's office controls, hold $400 million in Wal-Mart stock.