New York State Attorney General Eliot Spitzer filed a complaint against a mutual fund manager today alleging that the firm sanctioned numerous secret timing arrangements that cost small investors $80 million.

The attorney general’s office says that its lawsuit, filed today in State Supreme Court in Manhattan, refutes a claim by officials of the fund manager, J. & W. Seligman & Co., that there was only limited timing activity at the firm. The company made that claim last year, saying it had investigated itself thoroughly and found only four cases of timing arrangements that caused $2 million in damage to its investors.

The attorney general’s office disagreed and sought a court order requiring Seligman to provide documents and make employees available for testimony. The court granted that request and the attorney general’s office says that it uncovered 35 previously undisclosed agreements with mutual fund timers. These allegations have not been proven.

“While it is certainly within a company’s rights to continue to contest the evidence, the record shows that there was a clear breach of fiduciary duty at Seligman and that the company’s damage estimates are inadequate,” Spitzer said.

The Attorney General’s lawsuit, which names the company, its president, its fund distributor and shareholder services agent, seeks injunctive relief, disgorgement of fees and profits, and restitution, as well as penalties.