East German Communist Party chief Erich Honecker, in canceling a planned state visit to West Germany, appears to signal that relations between the two Germanys face a prolonged freeze.

East Berlin announced Thursday that its leader will not travel to Bonn in the fall for his first meeting with Chancellor Helmut Kohl "because of the situation brought about by West Germany." That was a reference to critical reaction by some conservative West German politicians and journalists to the deaths during the past three weeks of three West German citizens in East Germany. Two of them were being questioned by East German border guards.

Franz-Josef Strauss, leader of the Bavarian wing of the governing Christian Democratic Party and one of the most conservative West German politicians, called the death of Rudolf Burkhert, 46, on April 10 "a case of murder." He based the charge on the fact that a West German autopsy discovered a gash near Burkhert's temple.

Bonn asked for an official explanation and East Berlin authorities said Burkhert fell and struck a radiator when he suffered a heart attack at Drewitz, a control station just outside West Berlin. The city is an enclave 300 miles inside East Germany.

Strauss and the conservative media seized upon the incident to pressure the Kohl government to adopt a tougher line toward Communist East Germany. The conservative daily Die Welt raised a "serious suspicion" that Burkhert was "literally beaten to death." But the West German pathologist involved said the East German explanation was plausible.

Kohl, after phoning Honecker, also indicated that he was satisfied with the East German explanation. He said he also assured Honecker that Bonn would continue to make every effort to reach a closer understanding, according to a spokesman for the West German Embassy here. The two leaders also discussed overall East-West relations, particularly in the context of Kohl's recent visit to Washington, he said.

West German criticism intensified after another death of a West German was reported Wednesday. East German officials said Heinz Moldenhauer, 68, suffered a heart attack while being questioned by East German border guards about currency regulations. West Germans, including those using highways to West Berlin, must adhere to strict regulations in East Germany.

While no high official of the Kohl government suggested foul play on the part of East Germany in any of the cases--in the third, a woman died earlier this month while riding in a car en route to West Berlin--some officials pointed out privately that Communist border guards often appear unnecessarily intimidating to travelers.

A spokesman in Bonn said yesterday that Kohl found the cancellation of the Honecker visit "incomprehensible," Reuter reported. However, an East German source noted that East-West ties had been steadily deteriorating in recent years. He added, "We cannot foresee a climate suitable for an official state visit, particularly the first one" by the East German chief of state. The two Germanys initiated ties in 1971.

Ex-chancellor Helmut Schmidt and Honecker exchanged mutual assurances during a meeting in December 1981 in East Germany that they would try to improve relations. But the East German source, who declined to be identified, asked: "How can relations improve under the shadow of the missiles?" The reference was to the planned deployment of Pershing II missiles in West Germany starting at the end of the year.

Although the West German spokesman insisted Bonn would continue efforts to improve ties, such efforts appear to be falling victim to superpower politics.