"Today we can say that negotiations are a little bit behind schedule and probably we are already facing the necessity of transition or additional term of Brexit," she told reporters in Tallinn, which is hosting an EU summit.
UK and EU negotiators stated during the fourth round of talks this week that "decisive steps forward" had been taken, but more work was needed on both sides.
Officials want to conclude the talks on Brexit terms by March 2019 when the UK formally leaves the EU.
The most important issues for Brussels are Britain's Brexit bill, the fate of Northern Ireland and the rights of 3 million EU citizens living in Britain.
The latter issue is foremost in the mind of Lithuania, which has around 200,000 citizens living in the UK.
However, Grybauskaite said that Lithuanian would not stubbornly stick to its national interests, but would seek that a Brexit deal is acceptable to all countries.