"We regard (Minsk's statements) as threats that need to be taken seriously, because even though such threats sometimes seem strange or incomprehensible, we have seen these threats being carried out," Simonyte told a news conference.
"This was the case with the organization of illegal migration at the EU borders, as threatened by Minsk," she said.
The prime minister said that disputes must be resolved in a civilized and legal way.
"That would be the way to go," she said. "As to the threats, I don't know to what extent they will be realized, but we are assessing what impact they would have and looking at alternative solutions."
When asked what losses the economy might suffer if Belarus blocked trains from Lithuania, Economy and Innovation Minister Ausrine Armonaite said, "We don't know what specific retaliatory sanctions Belarus may impose".
"It's simply not possible to give concrete figures yet, because the situation is changing," she said.
Belarusian Prime Minister Roman Golovchenko said on Tuesday that Minsk would take tough retaliatory measures after Vilnius halted the transit of Belaruskali potash fertilizers via Lithuania.
Golovchenko said Minsk's measures would be targeted at trains coming from Lithuanian territory.
He also said that Belarus had invited Lithuania to hold consultations to define further relations.
According to Simonyte, the Lithuanian Transport Ministry has received an inquiry from Belarus' authorities under the countries' bilateral agreement on transit.
The US imposed sanctions on Belaruskali, one of the world's biggest potash producers, last August. The sanctions came into force in early December.
Lietuvos Gelezinkeliai (Lithuanian Railways, LTG) has terminated its long-term contract with the US-sanctioned Belarusian potash giant as of February 1 after the Lithuanian government ruled on January 12 that it was not in line with national security interests.