In a break with the Reagan administration's settlement policies, the chief of the Department of Education's office of civil rights has asked the Justice Department to begin enforcement proceedings against the state of Alabama because it had failed to submit an acceptable plan to desegregate the state's universities.

Assistant Secretary Clarence Thomas said in a statement yesterday that he was acting under a court order because the state had not filed an acceptable plan by an end-of-the-year deadline. It was the first time the department has refused to accept a state's settlement plan since the Reagan administration began. It has approved several others and is continuing negotiations with Kentucky, Ohio and Texas.

Joseph L. Rauh, an attorney for the NAACP's Legal and Educational Defense Fund Inc., which has forced the issue in court, said he was surprised at the announcement because he said the administration has accepted other states' plans that did little to desegregate university systems.

Alabama "must have gone back to the days of George Wallace standing in the schoolhouse door if their plan was rejected," Rauh said. He also questioned whether the referral to Justice was a legal maneuver because the NAACP is appealing the department's acceptance of a plan for North Carolina and the oral arguments are set for Friday.

Thomas wrote Alabama Gov. Fob James just before Christmas noting that the state delayed submitting any plan at all until Dec. 11, and that it contained only "vague commitments to consider undertaking unspecified steps some time in the future." It also wasn't signed by any of the state's 16 college and university presidents as required, he added.

Attorneys for the state could not be reached for comment yesterday.

On Jan. 7, 1981, the Education Department informed Alabama and several other states that its university system still showed signs of segregation. The two historically black schools in the state, Alabama State and Alabama A&M, were still 88 percent black, the staffs and governing boards of most schools were overwhelmingly white, and the allocation of state resources was unequal, the department charged in a letter to James.

The state spent large sums in recent years on new branches of the University of Alabama and Auburn near the existing black schools without similar efforts at the older, minority colleges, the letter said.

A spokesman at Justice said the department could file a suit against the state or enter into new negotiations for a settlement.