A new espionage dispute between West and East Germany erupted today over a prominent East German economist who faces spying charges after taking refuge in the East German mission here.

The economist, Herbert Meissner, who is deputy chairman of East Germany's Academy of Sciences, had sought to emigrate to the West a week ago after he was caught shoplifting in a West Berlin department store, West German officials said. But Meissner apparently changed his mind and decided to try to return to the East after he was flown to Munich and questioned by West Germany's intelligence service, the officials said.

Bonn government spokesman Friedhelm Ost said that West Germany would not allow Meissner, 59, to leave the country. The national prosecutor's office said that an arrest warrant had been issued for Meissner because he was suspected of spying.

The East German Foreign Ministry demanded Meissner's "immediate" return and accused the West German intelligence service of having staged a "forceful kidnaping" of Meissner.

East Germany's ADN news agency had reported earlier that West German agents had seized Meissner, but that he "was able to escape his captors and seek safety in the East German mission in Bonn."

The affair appeared certain to strain inter-German relations, which had shown some improvement in recent months, according to political sources here.

The incident became public when ADN reported yesterday that East Germany had protested to Bonn over the West Germans' "kidnaping" of Meissner. The East German report apparently came after Meissner had found shelter in the East German mission.

The West German government, which called the kidnaping accusation "absurd," hardened its stance on the case in the course of the day today. In his first comments to reporters, spokesman Ost said that Bonn officials were seeking to meet with Meissner to confirm that he genuinely wished to return to East Germany.

Later, however, Ost said that the meeting with Meissner had been canceled and that Meissner would not be allowed to leave West Germany. He said that "we have evidence" that Meissner was working for the East German Ministry of State Security, although he did not provide details.

Ost said that Meissner, after his arrest on the shoplifting charge in West Berlin, had asked to meet with the West German intelligence service. The economist was flown to the service's headquarters near Munich and was permitted to move about freely there, the spokesman said.

Meissner signed a statement saying that he had come to the West of his own free will, West German officials said. He was scheduled to meet yesterday with intelligence officials for a second round of talks, but failed to appear, they said.

The arrest warrant effectively confined Meissner to the grounds of the East German mission here. Bonn officials signaled that they would not seek to enter the diplomatic mission and arrest Meissner