"There will be attempts, and we are preparing for them, to deny residence permits to retired security servicemen," Vasily Svirin, head of the Russian team at talks with Estonia, told a news conference.
"We will press for the world community to recognize such attempts as illegal," Svirin said.
The presidents of Russia and Estonia signed two agreements Tuesday which provide for the withdrawal of the last 2,000 Russian troops from the former Soviet republic by Aug. 31 in exchange for permission for Russian military pensioners to stay in the country.
Svirin quoted the agreement allowing the pensioners to privatize their flats on an equal basis with Estonian citizens unless they "present a threat to the Estonian state."
The diplomat said Russia would only recognize expulsions in exclusive cases when there are "specific confirmed facts that a certain pensioner is involved in anti-government activities."
"We have asked the Estonian side why they do not start criminal proceedings if they have such facts," Svirin said. "There is no such evidence, they simply want all the pensioners to leave."
He criticized the Estonian government for employing the Stalinist concept of "collective guilt," blaming all former servicemen for the injustices of the 50-year Soviet occupation.
"Building relations with a neighboring country, especially one like Russia, on the basis of hatred, is, mildly speaking, irrational," Svirin said referring to comments by Estonian Prime Minister Mart Laar published in the newspaper Izvestia.
Laar said only part of the military pensioners would be granted residence permits in Estonia because "we believe that all the military pensioners threaten Estonia's security."
According to Svirin, Estonia has also postponed signature of an agreement to dismantle the nuclear reactor at the Paldiski naval base which had been scheduled for Wednesday afternoon.
Svirin said the Estonian side objected to a provision which would allow members of families of workers to stay temporarily after the work is finished if they have no housing in Russia or are receiving medical treatment in Estonia.
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