"We have informed them (Russia) that if they introduce a levy, they will do so as well. They do not object to this," Algis Zvaliauskas said on LRT Radio.
"Russian haulers will buy vignettes and pay accordingly, like everybody does in our country," he said.
An agreement between Russia and Lithuania now provides that truckers from one country do not pay for the roads of the other country.
According to Erlandas Mikenas, president of the Lithuanian national road haulers' association Linava, if Russia begins to charge Lithuanian companies before the interstate agreement has been revised, the State Transport and Transit Commission will have to decide, in consultation with the Foreign Ministry, on applying similar measures to Russian companies.
Zvaliauskas said that it remained unclear if Russia would start to charge the new fee on Nov. 15 or it would set out a transitional period.
According to the deputy minister, the new payment system will initially be applied in the Moscow region before being introduced nationwide in May 2016.
"The news from Russia is changing every half a day. It was said initially that we would pay 3.75 rubles, or around 5 cents, per kilometer, but the latest news is that we will pay 1.53 rubles, or just over 2 cents," he told the radio station.
Russia says that it is introducing a new system of payment for federal roads for vehicles over 20 tons.
Many Lithuanian road haulers have shifted their trucks to other countries after Russia imposed sanctions in August 2014.
