Russia can continue to transport sanctioned goods bound for its Kaliningrad exclave through European Union territory by train, but goods that serve a military purpose will be banned, the European Commission said on Wednesday.

EU member Lithuania, which lies between Russia and Kaliningrad, will only be allowed to block rail shipments of certain goods that have dual civilian and military use.

Russia can transport other goods on the EU's sanctions list, like iron and steel products, in regular quantities, a commission statement said, as it outlined new guidelines meant to de-escalate tensions with Moscow.

The instructions sent to EU member states carve out exemptions and come after Moscow chafed at a clampdown on some from freight shipments to Kaliningrad starting in mid-June.

The strategically important Russian exclave on the Baltic Sea is sandwiched between EU members Poland and Lithuania.

The threat of the coastal territory becoming increasingly isolated sparked concern in Moscow, as Kaliningrad's half million residents are heavily reliant on goods from mainland Russia. The Kremlin threatened countermeasures to punish the EU.

Road transport to Kaliningrad through EU territory remains prohibited under the EU modifications.

The European Union set out a transit ban on Russian goods in the bloc's territory as part of multiple rounds of sanctions since the invasion of Ukraine, some of which only started going into effect last month.

Russia had previously called Vilnius’ transit restrictions "illegal" and threatened the cancelation of the Russian-Lithuanian border treaty and the exclusion of Lithuania from a common electricity grid.

Brussels said transit volumes to Kaliningrad are now to be monitored closely, and if it is established that larger quantities of goods than usual are being transported, they are to be stopped.

This is intended to prevent Russia from transporting goods on sanctions lists via Kaliningrad to other countries and thus circumventing punitive measures.

Previously the European Commission had stressed that Lithuania's restrictions did not equate to a blockade, as claimed by the Kremlin, and was solely complying with EU sanctions. But, after protests from Moscow, Brussels later said it would review the guidelines.