SAN FRANCISCO—Time Warner has agreed to pay $400 million to five large institutions that opted out of a class action settlement of securities fraud charges stemming in part from unusual accounting practices at America Online.

The largest of the payments, $246 million, will go to the University of California. Smaller, but sizeable, settlements will be directed to the California Public Employees Retirement System, Amalgamated Bank, and two pension funds for Los Angeles County employees.

In 2005, Time Warner agreed to pay $2.4 billion to resolve a class-action securities suit against the company and $300 million to settle civil charges brought by the Securities and Exchange Commission.

The new payouts could rile some small investors because the institutions claim they are getting vastly better settlements than they would have had they remained in the class.

“We think it’s the largest single opt-out settlement in history,” an attorney for the University of California, Christopher Patti, said. “We think it’s between 16 and 24 times what we would have gotten through the class….It’s impressive by any measure.”

The school confirmed its settlement after The New York Sun inquired about a regulatory filing Time Warner made last week alluding to the deal, which is subject to approval by the regents. A spokesman for CalPERS, Brad Pacheco, said a “proposed settlement” was under review, but he declined to provide details.

The university and Amalgamated were represented by William Lerach of San Diego-based Lerach, Coughlin Stoia Geller Rudman & Robbins LLP. CalPERS and the Los Angeles funds were represented by Robert Kaplan of Kaplan Fox & Kilsheimer LLP. Mr. Patti said Mr. Lerach’s firm would receive about $37 million of the school’s settlement.

A law professor at Columbia, John Coffee, called the parade of large stockholders opting out of securities settlements “probably the most distinctive new trend in class action litigation.” Some of the institutions are taking advantage of state laws more advantageous than the federal law, but the professor said the wave of so-called opt-outs would reduce the amounts companies are willing to pay to the main pool of investors.

Mr. Coffee said the discrepancy in per-share recovery is “an embarrassing distinction” but one not easily rectified. “There’s virtually a constitutional right to opt out of the class,” he said.

The lead attorney for the class in the federal Time Warner case, Samuel Heins, did not return a telephone call seeking comment. Investors in the class have not yet been paid, but interest on the settlement is accruing.

Time Warner announced recently that late last year it added another $600 million to the existing $3 billion reserve for the company’s legal liabilities. The company said in a filing last week that all but $215 million of the $3.6 billion reserve was committed. It acknowledged facing another $3 billion in potential claims.

In December, The New York Sun reported that a $50 million settlement won by the State of Alaska was so lucrative as to cast doubt on whether Time Warner’s $3 billion reserve would be adequate. The firm gave no indication at the time that it was increasing the reserve.

A spokesman for Time Warner, Keith Cocozza, said Wednesday he could not comment publicly on the firm’s official filings.