Russia says it is pulling out of a border treaty signed with Estonia last month after nearly a decade of talks.
Moscow says it rejects clauses added by the Estonian parliament when it ratified the agreement on 20 June.
"Estonia did exactly what it promised not to do - insert political statements in the accord," said Russian Foreign Minister Sergei Lavrov.
Indirect references to the Soviet occupation were added, but Tallinn says the key treaty details were unchanged.
"Since the Estonian side has not fulfilled its obligations, we
withdraw our signature from this accord," said Mr Lavrov, speaking on a visit to Helsinki.
"There will be no accord... In order to regulate border issues,
we will have to restart negotiations," he added.
Both countries had signed a deal on 18 May fixing their land and sea borders after nearly 10 years of negotiations.
In 1940 Estonia was occupied by Soviet forces, who were driven out by Nazi Germany in 1941 but returned in 1944. Estonia remained part of the Soviet Union until 1991.
Estonia was one of 10 countries to join the EU in May last year.
Estonia also plans to join the Schengen zone of free travel in Europe, and anyone entering the country from Russia would be able to continue unchecked to most EU member states.
The agreed border is the frontier between Russia and Estonia as it stood when they were both republics of the Soviet Union.
Estonia had to give up 5% of its pre-World War II territory under the deal.
Russia has failed to reach a deal with another Baltic neighbour, Latvia, because of Latvian demands that the border be set according to a treaty signed in 1920.