The Cabinet on Wednesday decided to lodge a respective appeal to the EU General Court.
The Agriculture Ministry earlier proposed to contest the European Commission's decision that Lithuania failed to ensure adequate control procedures, saying that the EU's executive body incorrectly applied EU law and identified possible deficiencies only theoretically, according to a resolution drafted by the European Law Department under the Justice Ministry.
An appeal is to be filed with the General Court by July 12, it said.
The Commission's Directorate-General for Agriculture and Rural Development in 2009 carried out an audit to verify if Lithuania was making correct use of rural development funds.
The Commission said last May that it was claiming back 3.449 million euros in rural development funds from Lithuania due to "weaknesses in the on-the-spot controls".
It said that it was claiming back a total of 230 million euros in EU agricultural policy funds from 14 member states under the so-called clearance of accounts procedure.
The EU's executive body caries out more than 100 audits each year to check if EU funds have been spent properly.