"It's not the first time that the president has obviously taken a biased position and represents one very clear political party," he told reporters on Wednesday.
When asked what party he referred to, the prime minister said, "Let's make our own conclusions".
He reiterated that he would make his decision on Markauskas' staying in his post after receiving law-enforcement bodies' findings.
Skvernelis criticized Grybauskaitė for voicing her no-confidence in the agriculture minister while the prime minister was on a visit abroad. Before that, a presidential advisor met with Markauskas to urge him to resign.
Markauskas has come under criticism after media reports that his family used several plots of land without the landowners' permission and received EU payments for that land.
The minister says that his family farmed that land under an oral arrangement and that their failure to formalize the arrangement on paper was an unintentional mistake.
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