"I am surprised, because both the government and the Seimas have a very clear position on this issue," Skvernelis said on LRT Radio on Tuesday morning.
"Such statements are clearly not a defense of the interests of Lithuania in this case," he added.
The prime minister referred to Andriukaitis' statements, made in an interview with the Russian-language magazine Ekspress Nedelya in September, that Belarusians were more concerned than anyone else about the safety of the nuclear power plant because they had experienced the Chernobyl disaster first-hand.
The EU commissioner for health and food safety also said that Lithuanian politicians were mixing economics with politics when making decisions on boycotting the Astravyets facility.
Skvernelis underlined that Lithuania was putting in a lot of effort to make its position on the Astravyets project known both to its neighbors and Brussels.
Andriukaitis is the honorary chairman of Lithuanian Social Democratic Party (LSDP), the Lithuanian Farmers and Greens Union's junior partner in the ruling coalition.
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