MOSCOW (AP) _ Armenians ignored activists' calls for a strike Thursday to protest the Soviet government's rejection of their demand to annex a region in neighboring Azerbaijan, residents and the state-run media reported.

The reports suggested the government, after a five-month struggle, may be gaining the upper hand in controlling labor unrest that has caused millions of dollars in lost production in the southern republic of Armenia.

However, for the third night in a row, a large crowd of Armenians upset with the Kremlin's decision gathered Thursday in the central square of the Armenian capital, Yerevan, after working hours, according to one activist.

A former leader of the annexation drive, Igor Muradyan, told The Associated Press that ''a huge meeting'' took place with a prominent citizen he identified as Sergo Khanzodyan railing against Soviet leader Mikhail S. Gorbachev for failing to support Armenians on the issue.

The telephone line went dead before Muradyan could comment further, and repeated efforts to call to his and other Yerevan numbers met only busy signals.

Meanwhile, a 2-month-old strike was reported continuing in the disputed region, Nagorno-Karabakh, whose population is mostly Armenian.

The national television news program Vremya broadcast footage from Stepanakert, the region's administrative center, showing trucks and buses standing idle, construction sites empty and workers milling around the city.

Vremya showed hundreds of buses and trucks parked in protest of the decision Monday by the central leadership to keep the region within Azerbaijan. The broadcast blamed local officials for failing to encourage workers to return to their jobs.

''The people are embittered,'' said a worker with the Gostelradio state broadcasting authority in Stepanakert. ''We don't know what to do. But we know that the refusal to make Nagorno-Karabakh part of Armenia wasn't just.''

A correspondent for the official Soviet news agency Tass in Yerevan said the call for a strike beginning Thursday went largely unheeded.

''The majority of enterprises are working. It's a normal working day,'' said the journalist, who declined to give his name. Pressed to say whether anyone was striking, he conceded, ''Some enterprises are not working fully.''

Foreign Ministry spokesman Vadim Perfilyev told reporters at a briefing that industries in Armenia were nearly back to normal.

Khovik Vasilyan, an Armenian activist, said the strike call had no noticeable effect in Yerevan.

''The city today is working. Factories are in operation, and mass transit is running,'' Vasilyan, a former political prisoner, said in a telephone interview.

In a dispatch from Yerevan, a city of 1.1 million residents, Tass said that since Monday, ''more and more industrial enterprises of Armenia have begun to work at a normal pace.''

''Those who did not work or didn't work at their full capacity are returning to their jobs in Yerevan, Kirovakan and other cities,'' Tass said.

Armenians rallied Tuesday and Wednesday in Yerevan to show their displeasure with the Soviet leadership's decision.

On Monday, the Presidium of the Supreme Soviet, with Gorbachev's blessing, ruled that transferring Nagorno-Karabakh to Armenia would violate the Soviet Constitution, because Azerbaijan had objected to the move.

Nagorno-Karabakh has been part of the predominantly Moslem republic of Azerbaijan for 65 years, and Azerbaijani leaders had vetoed the region's decision to secede.

Armenians, most of whom are Christians, make up three-quarters of the 160,000 people of the contested region, and they contend that Azerbaijanis discriminate against them.

The annexation movement began in February after central authorities rejected an initial appeal from Nagorno-Karabakh. Strikes and mass demonstrations have plagued the region since then, at times triggering violence, such as the Feb. 28 riot in the Azerbaijani port of Sumgait in which 32 people were killed.

There was no word Thursday on the fate of Paruyr Ayrikyan, an Armenian nationalist.

Tass said Wednesday he was being deported for ''active instigation to inter-ethnic strife.'' Ayrikyan, 39, was arrested March 25 and charged with defaming the Soviet state.

Perfilyev told reporters he believed Ayrikyan was still in the Soviet Union but had received an invitation from a foreign country he did not identify.

Speaking in Washington, State Department spokeswoman Phyllis Oakley criticized the arrest and expulsion order but had no comment on the territorial dispute.

Asked if Ayrikyan was applying for admission to the United States, Mrs. Oakley said, ''We cannot confirm that Mr. Ayrikyan wishes to settle in the United States. Should he request to come here we would review his request sympathetically.''

However, a U.S. official speaking on condition of anonymity said Soviet officials had contacted the U.S. Embassy about the possibility of resettling Ayrikyan in the United States, where he has relatives.