The Department of Justice, in an unusual action that may violate its own guidelines, has subpoenaed telephone records of The New York Times' Atlanta bureau and of one of its reporters in connection with an investigation of news leaks to the paper, sources at both the department and the newspaper said yesterday.

The action, apparently authorized without the knowledge of Attorney General Benjamin R. Civiletti, was disclosed to the Times this week by the Atlanta office of Southern Bell, which by the law must report any such turnover of records to the government within 90 days.

Robert M. Smith, the department's chief press spokesman, said the action was authorized by Philip Hermann, head of the Criminal Division, and was done without following an elaborate set of rules seemingly designed to require approval from the attorney general and the deputy before subpoening notes or records from reporters.

In the past year, Civiletti has authorized a major internal investigation into leaks of Department of Justice materials in the Abscam case, and has authorized the use of polygraph tests on department employes in connection with that probe.

The rationale of the lawyers in the Criminal Division was that since the records were technically the property of the telephone company, not the reporter, the departmental guidelines did not have to be followed, Smith said.

Smith, who carries the title of special assistant to the attorney general, said his personal view was that Heymann's action was "in violation of the spirit of the regulation," and perhaps of the regulation itself. He also said that if the regulation really doesn't cover phone records, it ought to be changed.

"I can think of very few things that are more chilling to news gathering than trying to find out whom reporters speak to through their phone records," said Smith, a former reporter for The New York Times.

An attorney for The New York Times, Katharine Darrows, said the paper had sent a telegram of protest to Civiletti. "There's little or nothing we can do about the records now because they have them," she said. "But we want to make sure it doesn't happen again."

Department officials refused to tell the Times why the records, covering autumn 1979 to the end of March, had been subpoenaed. Several sources told Newsday, however, that they were sought as part of a probe of leaks involving a well-known FBI informant of the early 1960s, Gary Thomas Rowe.