Federal banking regulators are expected to announce new regulations today or tomorrow permitting savings institutions to pay higher interest rates than commercial banks on popular money market certificates.

Such action would shift money to the nation's savings and loan associations and mutual banks at a time when the profitability of such businesses has been reduced dramatically by the pressure of record interest rates.

At the same time, the decision would start channeling new money into the weak housing market, since thrift institutions are the major source of mortgage funds.

Commercial banks, however, will object strenuously to the decision. The bankers have been getting the lion's share of money market certificate volume since a previous interest rate differential was removed last March.

During the second quarter of 1979, banks got 53 percent of the certificates compared with a 32 percent share when S&Ls could offer higher rates.

According to informed sources, bank agencies will reinstitute a 0.25-percentage-point advantage for the thrift institutions -- the same level now required for passbook savings accounts. Current money market certificate rates for all the institutions are slightly higher than 11 percent, which would translate into an S&L rate of more than 11 1/4 percent.

As of Oct. 31, the money market certificates had brought in an estimated $114.6 billion to federally insured S&Ls since they were offered first in mid-1978. They now account for one-quarter of all S&L deposits. Growth was sharpest in late October, when S&Ls could offer as high as 12.65 percent on the six-month accounts, which require minimum deposits of $10,000.

Federal Home Laon Bank Board Chairman Jay Janis first revealed that banking agencies were considering restoration of the thrift institution advantage earlier this week. The differential was dropped last March so long as the certificate rate was 9 percent or more.

At the time, government officials were concerned about the cost to S&Ls of attracting new funds, but now -- with interest rates apparently having peaked and heading lower -- the goal is to bring more money back to the thrift industry and housing, for which a major recession has been forecast.

Willis Alexander, executive vice president of the American Bankers Association, sent a letter yesterday to Federal Reserve Board Chairman Paul Volcker, in which the bankers' spokesman warned in strong terms that a rate advantage for S&Ls "constitutes a ticking time bomb which will result in dramatic outflows of these most interest-sensitive funds from banks."

Separately, the bank board took another step yesterday to move money from Europe into the mortgage market by allowing S&Ls to borrow in the Eurodollar market and to secure such borrowings with mortgages.