"Lithuania has always taken the position that the Nord Stream 2 project is geopolitical, politically motivated, economically unjustified and tying the hands of some European countries in pursuing a free energy policy," the president told reporters on Wednesday as she arrived for NATO's summit in Brussels.
"We know that Russia always uses energy tools to influence domestic policies, too. Therefore, I think that such criticism is justified," she added.
At the start of the NATO summit on Wednesday morning, Trump lashed out at Germany, calling it "a captive of Russia" because of its pipeline deal with Moscow.
Germany has been a frequent target of criticism from Trump, who accuses Europe's biggest economy of spending too little on defense and freeloading on the US.
The American president on Wednesday also reiterated his wider accusations of NATO allies not paying enough for their defense.
Grybauskaitė called the US president's demand for allies to spend more on defense "quite legitimate".
"We've been talking about this since 2006, but many countries haven't even moved in that direction," the Lithuanian president said.
"I'm glad that we have moved closer to that target, we are investing in our defense and we can say now with our heads up that we support all of the remaining good initiatives for NATO modernization," she said.
Grybauskaitė added, however, that Trump's talk about Europeans' defense debt to the US is unfounded.
"This is probably a matter of rhetoric, because there are no formal agreements. These are gentlemen's agreements and understanding between partners that it should be invested this way. Really, there should be no talk about debts," she said.
Lithuania's leaders say that the country will this year meet NATO's 2 percent of GDP defense spending target. To achieve this, the government may have to increase the defense budget by more than ten million euros at the end of the year.