John M. Walker Jr., assistant secretary of Treasury for enforcement and operations since 1981, will leave the department to become a federal judge for the Southern District of New York on Sept. 9.

Walker played a key role in unlocking the Bank of Boston scandal in which Boston's oldest, largest and most venerated bank pleaded guilty to failing to report large cash transactions as required by federal law. Some of the transactions involved local reputed organized crime figures.

In an interview last week, Walker described a visit that he had with bank chairman William Brown earlier this month.

"We've never been able to establish a direct intent to launder money on the part of the Bank of Boston," Walker said. "Chairman Brown wanted to see me last week, and he came in here. He said at that time that he recognized the mistakes the bank had made, wanted to put the matter behind him, wanted to do what he could to restore the good name of the bank."

Walker added that Brown indicated that he "wanted to take a leadership position in the financial community and heighten awareness of institutions to the money-laundering problem and their need to get in compliance."

Asked why Brown couldn't take that leadership role without informing the Treasury Department, Walker replied: "I think he wanted to come in and go on record as being on our side. I don't think he's taking a hostile position to us or trying to pull the wool over our eyes. But on the other hand, what he does in the future will be the best measure of what he's saying now."

Last February the Bank of Boston agreed to pay a $500,000 fine after pleading guilty to charges of failing to comply with the Bank Secrecy Act in connection with the transfer of $1.22 billion in cash between the United States and Europe during a four-year period. Walker said that other banks may soon pay "substantial" penalties for failing to comply with the reporting requirements, but he would not name the banks.

IN AND OUT . . . Paul A. Bateman, formerly deputy assistant secretary of Commerce for economic development, has been appointed deputy U.S. treasurer. Bateman joined Commerce in 1982 as executive assistant to the assistant secretary for economic development and became deputy assistant secretary in May 1984. Before that, he served as deputy director for administrative operations in the White House's Office of Administration, and on Ronald Reagan's transition team.

Before joining the Reagan administration, Bateman was an assistant to former president Richard M. Nixon in San Clemente, Calif., and later in New York City.

Brien Benson, who had been the public affairs office's specialist on domestic finance and enforcement, has become director of the Energy Department's Office of Policy Planning and Analysis.

TAX REFORM UPDATE . . . The department is working to meet a Sept. 1 deadline for a report to Congress on revisions to its tax-simplification plan that would make it revenue-neutral.

The department's tax policy committee is working with the congressional Joint Committee on Taxation to come up with revisions that would raise $25 billion -- the amount Congress says the current administration proposal would cost the budget each year. President Reagan has vowed that his plan will neither increase nor decrease revenues.