Most Washington-area financial institutions said yesterday they will continue to offer interest bonuses on the new tax-free savings certificates despite a warning by the Internal Revenue Service that depositors could lose their tax exemption if they accept the package deals.

Elsewhere some major institutions, including Chase Manhattan Bank, have suspended their offers.

Of nine local depository institutions advertising the bonus plans, just two -- First American Bank in Washington and First Women's Bank of Maryland -- have suspended their bonus programs. The other seven will continue their offers unless the IRS rules against them. If it does, all said they would allow customers to withdraw their funds with accrued interest if necessary before Oct. 1 so as not to lose their exemptions. One question the IRS must decide is whether to make an exception for accounts established before its warning.

There was no word yesterday from the IRS on when a ruling can be expected.

In an unusual weekend announcement, the IRS expressed "substantial doubts" as to the tax consequences of investment packages linking short term retail repurchase agreements to the new tax-free All Savers certificates. The announcement was occasioned by advertisements promising annual interest rates of up to 40 percent and even 50 percent. In this way, banks and savings institutions hope to lure new customers in advance of the Oct. 1 starting date for the sale of All Savers certificates.

The offers have caused considerable confusion on the part of the public because the ads often do not make clear that the bonus rate, stated on a 12-month basis, lasts little more than one month. A 36 percent annual yield works out to a 3 percent return.

Yesterday there was also confusion and anger in financial circles. National Savings and Loan League president Richard S. Lawton declared, "This government by press release over a matter which (the IRS) has no discernible jurisdiction is irresponsible." He contends that the 1981 law creating the All Savers certificate does not empower the IRS to make any regulations relating to it.

IRS spokesman Leon Levine responded, "Unless specifically forbidden, the IRS has the authority to issue regulations under tax laws."

The argument voiced most frequently by those maintaining their offers is that the taxable retail repurchase agreement paying a high, unregulated, interest rate and the tax-free All Savers certificate, paying a lower, regulated rate, are two entirely different accounts even though buying a one-year savers certificate is usually necessary to reap the bonus. Interest is reported to the government on two separate forms.

The IRS warned the public that the package deals may violate the new tax law which sets time and interest limits on All Savers certificates. The yield may not exceed 70 percent of the investment yield on one-year Treasury bills. The bonus would push the total yield on the package over the limit. Similarly, by depositing funds a month early, a customer would be purchasing a 13-month certificate, not the prescribed 12-month certificate. Nonconforming certificates are not tax-exempt. Under the new law the exemption is $1,000 for individuals and $2,000 for married couples.

Participating banks and savings institutions reported good initial response to the offers. Interstate Federal Savings and Loan sold over $1.6 million in repos by promising 36 percent interest. A savings and loan across the street told of a customer who got a loan against his deposit there to invest his money in Interstate for a month. Unlike most institutions, Interstate does not make purchase of an All Savers certificate mandatory.

Some customers, duly warned, continue to invest, reported Columbia First Federal Savings and Loan, which is offering a repo at 36 percent without a mandatory link. However Jefferson Federal Savings and Loan reported "not a soul" showed up yesterday when television crews wanted to film the crowds.

In a related development, the Federal Deposit Insurance Corp., the National Credit Union Administration and the Federal Home Loan Bank Board yesterday authorized banks and thrift institutions to convert six-month money market certificates to tax-free All Savers certificates without imposition of a penalty for premature withdrawal.