The Federal Deposit Insurance Corp. on Tuesday exempted nearly all banks and thrifts from paying deposit insurance premiums for the second half of 1998.

Though 95% of banks will not pay premiums, reserves held by the Bank Insurance Fund are expected to grow 5 basis points, to as much as $1.43 for every $100 in insured deposits. Ninety-one percent of thrifts will not pay a premium, but the Savings Association Insurance Fund's reserves are expected to grow 9 basis points, to as much as 1.45% by yearend.

FDIC officials, however, warned at an open meeting that balances in both funds may fall next year.

Fred S. Carns, the agency's assistant director for insurance, said a 1996 law requires the FDIC next Jan. 1 to withdraw from the thrift fund everthing in excess of 1.25% to create a special reserve. This reserve is expected to total $850 million to $1.3 billion.

None of the FDIC board members expressed a position on the reserve, though director Joseph H. Neely did quiz agency staff members on how it would work.

He was told the reserve may be tapped if the thrift fund falls below 62.5 cents per $100 of insured deposits and the FDIC expects the fund to remain below that threshold for four consecutive quarters. "There is very little discretion," Mr. Carns said in an interview. "Our legal folks tell us that our hands are tied here."

The special reserve drew fire from the industry. Brian P. Smith, director of policy and economic research at America's Community Bankers, said the group hopes to include a repeal of this provision in the regulatory relief bill pending in the Senate.

"We would like to have this eliminated," he said. "We want the same rules to apply to BIF and SAIF."

Last week Joe C. Morris, chairman of the SAIF Industry Advisory Commission, urged House Banking Committee Chairman Jim Leach to commission a study on the need for the reserve.

Mr. Carns said the millennium computer bug will require the FDIC to increase projected losses for both funds next year. Though year-2000- related failures will not actually cost the FDIC money in 1999, he said the agency must increase its projected losses and that will drain reserves from the bank and thrift funds.

Responding to a question by acting FDIC Chairman Andrew C. Hove Jr., Mr. Carns said consolidation is unlikely to affect the insurance funds. The geographic diversity of megabanks offsets the greater risk of deposit concentration, he said.

Also at the board meeting, the FDIC adopted several rules to simplify deposit insurance coverage. Effective July 1, the agency will continue to insure for up to six months accounts held in the name of borrowers who have died. Currently, these funds immediately count against the coverage given to the heirs of the deceased. The agency also is loosening a requirement that agents inform the bank in writing when they are holding funds on behalf of a client.

Christopher L. Hencke, an FDIC lawyer, said the staff will propose rules to clarify coverage for joint accounts within the next few weeks.

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