A congressional study concluding that 20 of the nation's largest banks pay an average effective U.S. tax rate of 2.7 percent on domestic income received modest praise yesterday from the American Bankers Association.

John Garry, chairman of the ABA's taxation committee and a senior vice president at Morgan Guarantee Trust Co., said the staff of the Joint Committee on Taxation, which performed the study, "did an excellent job in a short time period."

The study, released on Wednesday, is expected to be used by Sen. Robert J. Dole (R-Kan.), chairman of the Senate Finance Committee, to build a case for increased taxation of the banking industry. The industry has the third lowest effective tax rate of the nation's major industries, according to the study.

Dole has threatened the tax hike in part as an effort to get the banking lobby to end a drive to pass a separate piece of legislation altogether: repeal of 10 percent withholding on interest and dividend income.

Garry, who is expected to testify at a Finance Committee session today, said: "The tax treatment of banking is a complex subject, even for tax professionals." His only criticism of the study, however, was to contend that "its utility is somewhat limited because it focuses on only 20 banks, all of them large institutions, and on only one year [1981]."

The Joint Committee analysis found, for example, that BankAmerica, the country's second largest bank, had U.S. income of $154 million in 1981, but got a refund or tax credit of $18 million. This translates into a negative tax rate of 11.7 percent.

Crocker National Bank got tax refunds or credits of $16 million, double the amount of U.S. income it received that year. This translated into a negative tax rate of 205.7 percent.

The primary mechanisms used by banks to lower or eliminate the federal taxes are tax-free bonds and investment tax credits and depreciation resulting largely from leasing deals.

The Joint Committee study did not count deferred taxes in calculating the effective tax rates. This method of accounting is disputed by officials of some corporations who contend they will have to pay the taxes in the future. Other tax experts counter, however, that every year banks and corporations added new deferrals, with the net effect that very little of the money is paid, or it is paid so long after the date the taxes were incurred that there is an effective major reduction in liability.