TALLINN, U.S.S.R. -- Packed into a small living room in this capital of the Estonian Republic, 70 members of the New World Church spent last Thursday evening in song and prayer, asking God for good health and long life, saving their most fervent plea for last: let the Kremlin free Estonia from Soviet rule.

The church, an unofficial group of 350 Estonian born-again Christians, has long annoyed the secular local Communist Party leadership with its twice-weekly sessions of Bible thumping and gospel singing.

But as nationalist sympathies rise throughout this small republic, occupied and annexed by Kremlin leader Joseph Stalin in 1939, local authorities are even more unsettled by the flat refusal of New World Church members to recognize Estonia as part of the Soviet Union.

The church, under the leadership of two Estonian evangelists, is part of the disparate movement of Baltic Separatists, political activists campaigning for the autonomy of the three republics along the Baltic coast: Estonia, Latvia and Lithuania. All were claimed by the Soviet Union in a secret 1939 pact with Nazi Germany, and all have been the scenes of mass demonstrations for independence in the past year.

While the nationalists were at first allowed to operate quietly under Soviet leader Mikhail Gorbachev's policies of greater openness and democratization, in recent weeks they have been subjected to a fierce crackdown, including media attacks, detentions and expulsions to the West. In anticipation of a demonstration in neighboring Lithuania on Tuesday in commemoration of the republic's declaration of independence 70 years ago, Soviet authorities have cut the telephone lines of dozens of local activists.

"We have even been warned against laying flowers on graves," Nijole Sadunaite, a Lithuanian activist, said in a telephone interview before her line went dead. "There are policemen and vigilantes gathering in the streets. Nobody is allowed to do anything. But we will try."

In the Soviet Union, whose 15 republics are composed of more than 100 ethnic groups, the Baltic separatists represent the tip of an iceberg. In regions such as the Ukraine and central Asia, residents have also been inspired by the Kremlin policy encouraging glasnost, or openness, and are increasingly public about the ethnic tensions dividing them.

By most accounts, the Estonian activists are a tiny minority in a small fishbowl, numbering no more than a few hundred in this republic of 1.5 million inhabitants, including 1 million Estonians. But in their opposition to Soviet rule they are nonetheless indefatigable. Last month, 14 Estonians officially applied to form a political party dedicated to the dissolution of the 1939 pact and to a free Estonia. They are seeking to organize another mass demonstration on Feb. 24, the 70th anniversary of Estonia's original declaration of independence. "It's clear now that either the Soviet Union is going to have to set Estonia free, or we will have to leave Estonia," Hubert Jacobs, a New World Church leader, said in an interview after services last Thursday.

Despite their fledgling status, the separatists have apparently caused alarm within the Communist Party leadership in Moscow. In recent months, they have come under heavy attack in the central state-controlled media, and according to unconfirmed reports, the ruling Soviet Politburo passed a resolution last December charging the Estonian Party with ideological shortcomings. This was widely interpreted as an order for local officials to stamp out dissidents, including the movement for Estonian separatism.

Since then, police in Tallinn and other Estonian cities have searched the homes of leading activists, detaining some and ordering others to leave the country. Earlier this month two Estonians seeking to start a new party were expelled to Sweden. When the residents of the Estonian city of Tartu gathered for a demonstration on Feb. 4, they were dispersed by policemen with rubber sticks, dogs and tear gas, according to witnesses.

One apparent reason for Moscow's harsh response is that calls for Baltic autonomy appear to strike a responsive chord among a wide number of Estonians and other natives of the region. A rally for Estonian independence held here Aug. 23 drew at least 4,000, according to dissident sources, and at least 800 showed up for the Tartu demonstration.

Anti-Soviet sympathies among residents have also apparently been aroused by the recent official publication of descriptions of some of the nasty aspects of early Soviet rule here.

Under the Kremlin policy of glasnost, in the past few months Soviet newspapers have for the first time published details about the deportation of Estonians under Stalin's leadership and other long-secret issues. The Estonian public reacted with outrage: in an official meeting of the union of writers late last fall, there were bitter complaints about the mass destruction of Estonian books by Soviet authorities.

Another reason for concern in Moscow is that Estonians have been among the slowest in the Soviet Union to assimilate with Russians, the dominant Soviet ethnic group and the largest minority here.

Despite an official drive to teach the Russian language, for example, only a quarter of Estonians speak the U.S.S.R.'s official tongue fluently, according to the latest official statistics. At the same time, only one of every 10 local non-Estonians speak fluent Estonian. "I would say that these two groups lead their own separate lives," said popular Estonian writer Udo Tuulik at a conference on the Baltics here last week, sponsored by the official Soviet press service Novosti. "Like the Mississippi and the Volga, we just flow in different directions."

With an annual influx of up to 8,000 Russians and other ethnics into the republic, however, native Estonians are beginning to feel they are losing ground to outsiders. In 49 years of Soviet rule, the percentage of Estonians living here has fallen from 92 to 61 percent, according to official statistics. In the past two years alone, the percentage of Estonians living in Tallinn has dropped from 52 to 50, and by the year 2020, the number of Estonians in the republic will likely plummet another 11 percent, according to official estimates.

The need to preserve things Estonian was the main factor motivating residents to try to start their own national independence party, according to Eve Parnaste, one of the founding members.

"With the number of Estonians living here steadily declining," she said in an interview, "there is just a little time left for us to try to return Estonia to what it was and to keep it pure."

The local party, too, has responded to the threat of another surge of outsiders. On Jan. 20, the Estonian Central Committee passed a package of measures to reduce the influx of immigrants from Russia and other parts of the Soviet Union.

The key new regulation requires local firms to pay the state 16,000 rubles for every employee they bring from another republic, and an additional 16,000 for each family member. A family of four moving from Russia to Estonia would cost an Estonian enterprise 64,000 rubles -- more than $100,000.

"We probably cannot cut immigration altogether," said Arvo Kuddo, a demographics expert at the Estonian Academy of Sciences, during the Novosti-sponsored conference. "But what we're trying to do is limit it."

According to interviews held last week with Estonians, the new measures may still be insufficient to combat the anti-Russian sentiment here.

Even in the New World Church, with its emphasis on Christian values, separation between Russians and Estonians is strictly observed. Church members shun Russian for instance, preferring English or German when not speaking in Estonian. With the faithful gathered around him in his Tallinn home, New World Church leader Jacobs was asked whether Russians would be allowed to join. "No," he said flatly, "But we would pray for them."