"Many people left town this morning," said a spokesman for the Estonian rescue service in Paldiski.
Admiral Alexander Olkhovikov, head of the Paldiski naval base, told a news conference Tuesday that the operation to dismantle the reactors could last for up to three months.
The fuel rods would leave Estonia by special train after work to dismantle the second reactor had started.
The base, across the Gulf of Finland from Helsinki, was the main nuclear-submarine training base of the former Soviet Union.
Dismantling its two reactors and removing their nuclear fuel rods is one of the final stages in the operation to withdraw Russian troops from the Baltic state after five decades.
The last combat soldiers are due to leave Estonia and Latvia next week, although some 200 specialists will remain in place to oversee operations at Paldiski base until next September. Estonia is planning to mark the departure of the last Russian troops with rock concerts, pea soup and church services.
Prime Minister Mart Laar and President Lennart Meri said expensive state functions Aug. 31 to mark the final day of the pullout had been canceled.
The president recommended that he "have the Estonian army's traditional pea soup at the army barracks instead of champagne at an official function," said a statement from Meri's office.
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