The program, agreed in the run-up to Lithuania's accession to the EU, allows Russian citizens travelling by rail between mainland Russian and the Baltic Sea exclave of Kaliningrad to cross Lithuania under a facilitated procedure. They are issued with transit documents by Lithuanian consular officials on trains.
Lithuania is seeking 215 million euros in EU funding for the program in the bloc's 2021-2027 budget. European Council President Charles Michel has proposed 139 million euros.
"Since 2005, more than 6 million Russians (more than a thousand per day) have benefited from the EU-Russia special transit scheme, which in practice is fully implemented by Lithuania, using Lithuanian manpower, Lithuanian infrastructural facilities etc.," the foreign minister said in a statement to BNS.
"It is a security issue and if it remains underfunded as it is now, it may jeopardize EU security," he said.
EU leaders began talks on the bloc's new budget on Thursday evening.
Lithuanian President Gitanas Nauseda said before the talks that he would demand adequate funding for the Kaliningrad program, but added that Lithuania would act responsibly.
When asked by BNS if Lithuania would consider stopping the transit at a certain point if it does not receive the necessary funding, the president said: "We are a responsible member of the EU and implement our obligations responsibly, but at the same time, we demand adequate financing of these functions".
"Lithuania is not rich enough to fund the common needs of the EU at its own expense," he added.