"I think the six-year period will not be easy in terms of interstate relations," Skvernelis told reporters on Monday.
"I think the dialog will certainly not be easy as regards Russia as a state, within the EU framework, from a transatlantic perspective and in terms of relations with neighbors. It won't be a simple period," he said.
According to the Russian electoral commission, Putin won his fourth presidential term with over 76 percent of the vote, with the official turnout at 67 percent.
Lithuanian Foreign Minister Linas Linkevičius said earlier on Monday that "the ongoing process cannot be considered as free and democratic elections".