The federal government began administrative proceedings yesterday that could eventually lead to the loss of millions of dollars annually in higher education aid by the state of North Carolina.

Joseph A. Califano Jr., secretary of health, education and welfare, said he is taking the action because the state has failed to submit an acceptable plan to desegregate its 16 senior colleges and universities.

North Carolina is the only one of six states that has failed to present an acceptable college desegregation plan to HEW in compliance with a court order.

Califano said he will delay giving any new grant money to the state's four-year colleges if the federal funds "would contribute to continuing segregation" in the state system.

A HEW official said the deferral could affect new grant money for continuing programs. Student aid will not be affected, Califano said.

He said the deferral of new grant applications will be reviewed on a case-by-case basis by HEW's general counsel and the Office for Civil Rights.

Califano said he didn't know exactly how much the state would lose in higher education aid. The 16 institutions received $68 million in federal funds in 1977.

North Carolina officials immediately expressed disappointment in Califano's decision.

William B. Friday, president of the state's university system, said, "The secretary's decision is deeply disappointing and we believe it is wrong."

Friday said the state already is committed to "equality of educational opportunity to all citizens regardless of race."

He said the talks between HEW and state university officials during the past few weeks appeared to be "productive." However, he said the secretary's action makes it "questionable whether we can or should continue discussions."

In February, Califano gave the state an additional 45 days in which to negotiate a satisfactory five-year college desegregation plan with HEW.

HEW wants the state to increase its black enrollment at the 11 predominantly white colleges and its white enrollment at the five predominantly black colleges; to increase the black faculty members at the predominantly white institutions; to eliminate duplication of programs at the predominatly black and predominantly white colleges in the state, and to strengthen the predominantly black colleges by giving them new resources and programs.