Banks could be prohibited from operating mutual funds for Individual Retirement Accounts as the result of a federal district court decision handed down last week in San Francisco.

Only three banks have set up pooled IRA funds so far, but others were eyeing the practice, which was approved by the Comptroller of the Currency last February.

However, U.S. District Judge William W. Schwarzer last week set aside the comptroller's decision that allowed Wells Fargo Bank and Bank of California to establish comingled stock funds for customers' retirement dollars. He ruled that the comptroller's order violated the federal Glass-Steagall Act, which forbids commercial banks from marketing securities.

The comptroller exempted IRA pooled accounts from rules governing trust funds so the IRA mutual funds could be registered with the Securities and Exchange Commission. The judge ruled that the mutual funds were really "investment vehicles" in competition with mutual funds and therefore illegal.

The case was brought against the comptroller by the Investment Company Institute, the trade organization for mutual funds. Yesterday the institute declared, "This decision is a major rejection of attempts by banks to evade national policies requiring the separation of commercial banking and securities activities."

A spokesman for the Bank of California said he was "very disappointed." He said the bank is considering whether to appeal or to ask for a stay pending an appeal. The comptroller's office said it is still studying the court's ruling.

A similar case against the comptroller, involving IRA accounts at Citibank, is now pending in federal court in Washington.