LONDON, June 21 (Reuters) - A top ally of President Vladimir Putin told Lithuania on Tuesday that Moscow would respond to its ban on the transit of goods sanctioned by the EU to Russia's exclave of Kaliningrad in such a way that citizens of the Baltic state would feel the pain.

With relations between Moscow and the West at a half-century low over Russia's Feb. 24 invasion of Ukraine, Lithuania banned the transit of goods sanctioned by the European Union across its territory to and from the exclave, citing EU sanction rules.

Nikolai Patrushev, a former KGB spy who is now the secretary of Russia's Security Council, said Lithuania's "hostile" actions showed that Russia could not trust the West, which he said had broken written agreements over Kaliningrad.

"Russia will certainly respond to such hostile actions," Patrushev was quoted as saying by state news agency RIA.

"Appropriate measures are being worked out in an interdepartmental format and will be taken in the near future," he was quoted as saying. "Their consequences will have a serious negative impact on the population of Lithuania."

Lithuania, a member of NATO and the European Union, said it was simply applying agreed EU sanctions on Russia, adding it was "ironic" to hear Moscow's complaints given its war in Ukraine.