According to Roger L. Barnes, Fannie Mae, the giant mortgage finance company where he worked as an accountant for more than a decade, used "threats, intimidation and reprisal" against him and others who raised concerns about the company's accounting.

In a 25-page statement released yesterday at a House Financial Services subcommittee hearing, Barnes described what he called a three-year effort to convince senior Fannie management, including chief executive Franklin D. Raines and Chief Financial Officer J. Timothy Howard, that the company's system for accounting for amortizing certain expenses and fees, a key element in its profitability, was seriously flawed and being manipulated to meet earnings targets.

Barnes, who did not testify in person at the hearing, alleged that Fannie's internal auditors only reluctantly addressed his concerns and that the internal investigation of the accounting was inadequate. While the company promoted those who helped "suppress the truth" about the irregularities he reported, he said, he was stripped of duties, downgraded in performance reviews and "ultimately forced from the company."

A recent report by Fannie's regulator, the Office of Federal Housing Enterprise Oversight, said Barnes's complaints were substantive and his "cooperation was important" in its investigation.

Barnes declined through his lawyer, Debra S. Katz, to comment beyond his statement. Katz said Barnes has been asked to meet with investigators at the Securities and Exchange Commission and the Department of Justice. Both agencies are probing the accounting practices criticized in OFHEO's report.

Fannie Mae spokeswoman Janice Daue declined yesterday to comment on the specific allegations in Barnes's statement. She added, "We took his issues very seriously when they were raised."

An employee at Fannie since 1992, Barnes's job in the late 1990s put him in charge of making sure the company was properly accounting for changes in certain amortization costs in its mortgage business. The job required particular knowledge of Financial Accounting Standard 91, which deals with complex calculations of estimating how and when expenses and fees, incurred when a mortgage is bought or originated, are booked over the life of the loan.

For Fannie, with more than $900 billion in mortgage-related assets, implementation of FAS 91 was a critical accounting policy that, when the expected life of a mortgage asset changed, resulted in recalculations of expenses and income. Under the rule, rapid changes in interest rates can cause wide swings in amortized costs and income, creating earnings volatility.

When the company implemented a new system to determine the rate for amortizing the expenses and income associated with its mortgage products, Barnes said, he raised concerns. He said the system appeared to be designed in part to help "manage" Fannie Mae's recognition of expenses and income -- to, in effect, help the company manage its bottom line.

Barnes said Fannie's announced policy of fair treatment for employees is different in reality. "The atmosphere and culture . . . is one of intimidation, restraint of dissenting opinions and pressure to be part of the 'Team,' " his statement said.

Roger Barnes, with his attorney, Debra Katz, says he tried to persuade Fannie Mae to change its accounting system.