"The Commission president assured the head of state that Lithuania would be able to apply to the European Commission for aid to affected farmers," her press office said.
More than 10 Lithuanian municipalities have already declared an emergency situation over damages caused by heavy rainfall and it is planned to declare a nationwide emergency this week.
The Agriculture Ministry estimates that farmers' losses due to the rainy weather may reach around 40 million euros, but the Chamber of Agriculture puts the figure at some 180 million euros.
Grybauskaite and Juncker met in Tallinn, which is hosting an EU summit.
According Grybauskaite's office, the Lithuanian president also sought support from the European Commission for the planned electricity grid synchronization with the Western European system.
The three Baltic nations aim to disconnect their grid from the post-Soviet energy system and synchronize it with the European electricity system within the next decade in a bid to reduce their dependence on Russia.
However, the initiative has lately faced difficulties, as Lithuania, Latvia and Estonia disagree on how to connect their grids to the Western European system.
Vilnius has recently warned the neighboring countries that Lithuania will not wait for their decision and will synchronize its power grid with Poland on a bilateral basis.
The Lithuanian government does not have enough money in its reserve to cover farmers' losses due to heavy rainfall, Prime Minister Saulius Skvernelis said on Friday.
"If we take specifically the government's reserve, (which amounts to) around 1.5 million euros, then it is simply impossible to compensate for these losses. However, this reserve will be opened up if we find a way of easing the burden for farmers," he said after meeting with farmers in the town of Ukmerge.
Skvernelis said that Lithuania would apply to the European Commission for compensation, but added that he was not sure if Brussels would provide funds, noting that the Commission had not helped drought-stricken Southern Europe.
On the other hand, Lithuania receives less support than old EU member states, which could become an argument in seeking compensation, he said.
According to the Agriculture Ministry’s preliminary estimates, farmers' losses due to the rainy weather may reach around 40 million euros.
