Several dozens pupils were at their seats, their names on cards in front of them, when the teacher strolled in at 3 p.m. and took his place beside the flag and the blackboard.

By his own reckoning it had taken 20 years, but the biggest gun in American education yesterday became an honest man again.

Ernest I. Boyer, the U.S. commissioner of education, returned to classroom teaching.

Boyer's pupils were employes of the U.S. Office of Education, and the boss of the agency was there to begin a short course on the use of clear language.

Three different groups of Office at Education bureaucrats will go through Boyer's three-hour course, which he set up to help flush gobbledygook out of his agency.

The commissioner's effort happens to coincide with President Carter's frequently stated wish that federal employes clean up their language - that is, make it understandable.

Boyer explained that his distaste for gobbledygook is long standing, but it was also clear that his experience at the Office of Education since early last year has been jarring.

He told of memos and communications reaching him from the bowels of the bureaucracy, written in a jargon he cannot understand. Ten times a day, he said, he tells visitors to his office to restate their ideas because they're not coming through.

By way of illustration, the commissioner brought samples of bureaucratic gibberish from his desk.

One sentence rambled through 38 words to say "we have no money" without actually saying it.Another 55-word paragraph tried to say "we have people who could help" but never said it. One phrase described students as "the raw material we are inputing . . ."

The trouble with this language, Boyer told his class, is that it is worse than undecipherable. It contributes to the public's continuing loss of faith in governmental agencies.

"It inhibits communication . . . reinforces the very attitudes that people bring toward bureaucracies as faceless, obscure organizations," he said. "People conclude it is not a human, living, breathing organization."

Some of Boyer's pupils nodded dutifully.

"I notice your nods," he said. "That gives me reassurance. I got more As in graduate school by nodding when I thought I should - and even occasionally applauding."

There was no applause yesterday, but by the time he was halfway through his lecture, Boyer had shed his jacket and the class was asking questions and challenging him.

"The more specific we are, the better the attitude will be toward this organization and the better our relationships with ourselves will be," he said.

Boyer said he would like to see several changes in the writing habits at the Office of Education - put some emotion (fear, frustration, affection) in the memos and letters; remove "the cloak of impersonality . . . of something called 'the office.'"

Heads were nodding in approval.

For homework, Boyer told his students to scan their in-baskets for examples of "mild absurdity" in bureaucratic writing and bring them to class. "Just don't tell your boss," he cautioned. "I'd like for you to be my spies."

Lecture over, the commissioner slumped a bit of his desk but he was loving it.

"I had intended to have a coffee break midway through, but I got carried away," he said. "I can't believe that after 20 years I became an honest man again today."