Only a certain volume of sanctioned Russian goods, intended for civilian use only, will be allowed through the EU and into Kaliningrad.
The European Commission on Wednesday released new guidance on the transit of goods from Russia to its Kaliningrad exclave in what is seen as a bid to defuse tensions.
The Commission said that although the transit of sanctioned goods by road with Russian operators is not allowed under the EU measures, "no such similar prohibition exists for rail transport, without prejudice to Member States' obligation to perform effective controls."
It said that certain sanctioned goods deemed essential such as iron and steel, cement and wood, coal and crude oil can transit through the bloc between Russia and its exclave on the Baltic Sea provided the volumes transported "remain within the historical averages of the last 3 years."
This is to reflect "the real demand for essential goods at the destination" and ensure that "there are no unusual flows or trade patterns that could give rise to circumvention," it added.
However, it stated that the transit of sanctioned military and dual-use goods and technology remains fully prohibited regardless of the mode of transport.
Moscow had lashed out at Lithuania, which borders Kaliningrad and Belarus, after the Baltic state started thoroughly checking Russian cargo transiting through its territory. Vilnius, meanwhile, had emphasised it was respecting EU sanctions and not over-stepping.
Weeks of talks at the EU level ensued to clarify the bloc's position.
Under the sixth round of sanctions imposed by the EU against Russia for its unprovoked military attack against Ukraine, the 27-bloc has banned the export of certain EU goods to Russia.
These include cutting-edge technology, especially if it can also be used by the military, certain types of machinery and transportation equipment, technology needed by the aviation or maritime sectors, specific goods and technology needed for oil refining or the energy sector as well as luxury goods.
Meanwhile, the EU has also prohibited imports from Russia into the EU of coal and other solid fossil fuels, steel and iron, wood, cement, crude oil and refined petroleum products.
All these goods are also forbidden from transiting through the EU.
The EU's executive stressed that although the transit of these essential, albeit sanctioned, goods are permitted between Russia and Kaliningrad, "member states are under the legal obligation to prevent all possible forms of circumvention of EU restrictive measures."
This means that Lithuania must continue to monitor two-way trade flows "between the noncontiguous parts of the Russian Federation" through "targeted, proportionate and effective controls and other appropriate measures" to prevent violations of EU sanctions.
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