The State Department yesterday lifted two of the sanctions imposed against Chile in the aftermath of the 1976 murder here of Orlando Letelier. The move drew protest from government prosecutors and raised questions about the consistency of the Reagan administration's campaign against terrorism.

The action caused lawyers in the U.S. attorney's office here to charge that the military regime of President Augusto Pinochet is being "rewarded" for obstructing American justice.

It also led human rights advocates to question whether Secretary of State Alexander M. Haig Jr.'s top-priority emphasis on combating "international terrorism" will be applied not only against communist countries such as the Soviet Union and Cuba but also against rightist regimes such as that in Chile.

Specifically, the department said it was ending the ban on Export-Import Bank financing for U.S.-made products sold to Chile and inviting Chile to resume participation in the annual joint exercises conducted in the Pacific by U.S. and Latin American naval forces.

These were part of the sanctions imposed by the Carter administration in November 1979 in retaliation for Chile's refusal to extradite three former police officers under U.S. indictment for complicity in the car-bombing murders of Letelier and his American associate, Ronni Moffitt.

State Department officials said yesterday that the sanctions were being lifted to further U.S. commercial and security interests in Latin America.

However, the action drew an immediate and unusual public protest from Lawrence Barcella, one of the two assistant U.S. attorneys who headed the Letelier investigation. In an interview, he called the move "very unfortunate" and added:

"The original reason for the sanctions was to protest the Chilean government's total inaction and totally irresponsible investigation over the 20 months preceding the sanctions. Today's action could be viewed as rewarding Chile for its continued intransigence and failure to do anything worthwhile in the ensuing 15 months."

When the State Department originally imposed the sanctions, it said Chilean authorities had "in effect condoned an act of international terrorism."

At a highly publicized news conference last month, Haig declared war on "international terrorism," and the Reagan administration has been using that term as justification of its efforts to halt what it claims is massive outside communist support for leftist guerrillas in El Salvador.

The outward inconsistency of the administration's approach was pointed out yesterday by several human rights activists and congressional liberals.

Typifying their reaction was a statement by Sen. Edward M. Kennedy (D-Mass.), who noted that the administration has made antiterrorism "one of its highest priorities" and added that "the administration has failed the first test in the case of Chile."

Sen. Claiborne Pell (D-R.I.), ranking minority member of the Foreign Relations Committee, said he was very disturbed that the committee had not been consulted or informed in advance about the move. He added: "By the revocation of this measure against Chile, the new administration is setting a bad example for its campaign against international terrorism."

At issue has been Chile's refusal to send here for trial in U.S. District Court the three officers indicted by a grand jury on charges of planning the murder of Letelier, an exiled leader of the Chilean left. Letelier and Moffitt were killed Sept. 21, 1976, allegedly by an American agent of the Chilean secret police working with three Cuban exiles.

Other sanctions imposed in 1979 involved reducing various official diplomatic, economic and military ties with Chile.

These remain in effect, but State Department sources said yesterday that the Reagan administration has decided it is time to improve relations with Chile, and they added that the other measures are being reviewed with an eye to their gradual removal.