Then new U.S. commissioner of education yesterday ordered a major reorganization of the Office of Education, declaring the administrative structure he inherited to be "cluttered and confusing . . . impossible to monitor."

Over the years, Commissioner Ernest L. Boyer told reporters, each administration has added special assistants and pet programs to the commissioner's office, "leading to duplication of programs and competition for access and authority."

By the time he took office April 1, Boyer said, the Office of Education's organization structure had reached the point where 28 people representating 26 staff offices were assigned to his immediate office and reported directly to him.

Calling that arrangment "impossible," Boyer announced a series of program and policy consolidations and realignments reducing to seven the units reporting directly to the commissioner.

"This move will strengthen the commissioner's office and elimiante a top-heavy bureaucracy," he said.

In a prepared statement, Health, Education and Welfare Secretary Joseph A. Califano Jr. called the Office of Education reorganization "the second major step that the Department of Health, Education and Welfare is taking to fulfill President Carter's campaign promise ot make the government more efficent and more effective . . ."

The first step, a spokesman said, was Califano's March 8 announcement of a sweeping reorganization of HEW.

"De. Boyer is sweeping away the clutter that has confused policy direction and management in the Office of Education for too long," Califano said.

In specific terms, Boyers said, the reorganization will consolidate into two new offices the duties now assigned to eight units within the commisioner's office.

Four programs dealing with women and minorities - black concerns, Spanish speaking programs, women's programs, and programs for Asian and Pacific Americans - will be remade intoan Affirmative Action Office, Boyer said.

Among the duties of that office, he said, would be creation of the first comprehensive affirmative action plan for employment within the Office of Education itself. Additionally, that office would be responsible for seeing that program policies and services delivered by other units within the agency reflect the Office of Education's commitment to affirmative action.

A second new office will be called the Education Community Liaison Office and would replace four separate staff offices that attempt to relate the Office of Education to educational constituencies across the nation. The new office would attempt to link the Office of Education with state school officials, local superintendents, other educational groups and concerned citizens.

A major effort in this area, Boyer said, would be to cut down on the amount of paperwork local school officials have to perform to apply for federal grants or to comply with federal regulations.

Declaring the local frustration over federal red tape had reached crisis proportions, Boyer asserted, "The aim here is to get money to schools and help children and I think we have a great dealof cleaning up to."

Boyer, who became commissioner of education after seven years as chancellor of the 350,000 student State University of New York, said his reorganization plans are aimed at improving three broad areas of education. These are improved access for women, minorities and other "historically bypassed," improving the teachning of such basic as reading, writing and mathematics, and seeking new directions, including extension of education programs into communities and homes.

Other aspects of the reorganization, Boyer said, will be continuation of the staff units handling public affairs, legislation and policy studies, and the appointment of two senior deputies, one to coordinate programs and the other to supervise program supports.

Boyer said he anticipated the reogranization could be accomplished without dismissing any of the agency's 3,000 employees. The Office of Education spends about $9 million a year.