With his annual federal salary and government pension totaling $78,225, a civil servant is drawing around $12,000 a year more than his boss, Secretary of Health, Education and Welfare Joseph A. Califano.

Thomas L. (Lem) Johns, 52, who headed the Secret Service detail that guarded President Lyndon Johnson, is one of a number of federal law enforcement aides who are permitted to benefit from a special D.C. retirement system.

Condemned recently by the General Accounting Office (GAO) as too generous and costly, the system allows its retirees to draw full pension, plus full federal salary, when they begin second careers in government - a variation on the practice known as "double-dipping."

Johns' federal salary as a senior grade 15 is $47,025 a year. He also gets a pension of $31,200 a year for his 21 years with the Secret Service.

The GAO has recommended that the special pension system be scrapped, at least where it applies to federal employees. Designed for D.C. police and firemen, the plan also covers about 1,500 federal law enforcement employees in the Executive Protective Service, the U.S. Park Police and the Secret Service. They get higher pay and "much better" retirement benefits than their federal civil service counterparts, the GAO report says, and yet they contribute less money to the plan and are required to work a shorter time.

Johns yesterday confirmed through spokeswoman the pay and pension figures, which were reported in an Associated Press story. GAO, in its investigation, had estimated his pension to be closer to $18,000.

If Johns had retired under the regular civil service system, his HEW salary would have been [WORD ILLEGIBLE] the full amount of his pension.

President Carter has criticized the practice of [WORD ILLEGIBLE] , which is more often associated [WORDS ILLEGIBLE] officers who retire from the military, join the government and draw both pension and salary.

Under the special D.C. pension plan, Johns' combined federal pay and pension enables him to outearn members of Congress ($57,500) and top-ranking civil servants ($47,500). He also gets more than Vice President Walter Mondale ($75,000). Califanos Cabinet pay is $66,000.

When Califano appointed Johns last March to be his administrative officer, some press reports called Johns a highly paid "bodyguard." Califano at the time called such a description of Johns' duties "utterly unfair and irresponsible."

Califano, formerly a prominent Washington lawyer, was a top adviser to President Johnson at the same time Johns was in charge of Johnson's security.

According to HEW spokeswoman Eileen Shanahan, Johns' primary duties include managing the more than 100 employees in the office of the secretary and handling a variety of paperwork for the office, including the budget, procurement and other matters.

Johns also travels with Califano and has "personal security" duties on those trips, Shanahan said.

Regarding reports that Johns carries a handgun, Shanahan confirmed that he had worn one on at least one overseas trip with Califano but that "as a general rule, certainly, not around here in his capacity as an administrative officer."

It has been years, she said, "since this man has been just a bodyguard for anyone," adding that his White House security job, where he and Califano became acquainted, was actually an administrative post.

Johns refused to talk to a reporter, and more than one HEW aide indicated that he, being an old Secret Service hand, "never talks to the press."

Johns reportedly has told acquaintances that he was unhappy when Richard Nixon took office and removed him from his White House security post, even though the job supposedly was "non-political." At that time, Johns was made chief of the Secret Service office in Birmingham and retired from there in 1976, reportedly on disability following a heart attack.

It was Califano who suggested to President Carter that the government's pension systems are "irrational," Shanahan said, after which the president appointed a task force to study the problem.

"But I don't see the point in focusing on a single individual who happens to be legally taking advantage of the system," she said. CAPTION: Picture, Thomas Johns' salary, pension total $78,225, AP