Artis Pabriks, Latvia's Defence Minister, linked the deployment to the broader cooling in relations between the EU and Russia as well as the long-running dispute between Moscow and Nato over missile defence.
"It creates unnecessary political tension and suspicions and reduces mutual trust because we don't see reason why Russians would need such weapons here," he said. "I think it's just to show who is the boss in the region."
Russia warned in 2011 that it might put Iskanders in Kaliningrad in response to the Nato plan but did not made any official announcement until after the missiles were seen close to Poland.
The Polish Foreign Ministry said the deployment was "worrying" and would "undermine constructive dialogue" with Russia.
Lithuania, which is chairing EU "eastern partnership" talks with Ukraine, has also expressed fears that the missile deployment will increase tensions between Europe and Russia.
"I am worried about signals that Russia is about to modernise missile systems it has deployed in Kaliningrad," said Juozas Olekas, Lithuania's Defence Minister. "Further militarisation of this region, bordering the Baltic states and Nato, creates further anxiety."
Prospects of the EU signing a trade deal with Ukraine receded further as Viktor Yanukovich, the Ukrainian President, signalled he was ready to sign a loan and cheap energy deal in Moscow today.