"The president considered Savickas' candidacy for the post of economy and innovation minister and he made the decision not to approve his nomination," Antanas Bubnelis, Nauseda's spokesman, told reporters on Wednesday.
Skvernelis nominated Savickas on January 24.
Savickas, 29, is the prime minister's advisor on economic affairs and strategic change management. He was last year elected to the City Council of Vilnius on the ticket of the Lithuanian Farmers and Greens Union, but is not a member of the party.
His past career includes positions at the government's foreign investment promotion agency Invest Lithuania, and Investors' Forum.
The post of economy and innovation minister has been vacant since last December, when Virginijus Sinkevicius became a European commissioner.