"The president underlined that the initial proposal put forward by the Commission was unacceptable to Lithuania and many other countries," Grybauskaitė's office said in a press release.
"Lithuania seeks to make EU payments consistent with the level of development of member states in order to eliminate the existing economic and social differences between them," it said.
Lithuania mostly criticizes the proposed budget for not earmarking funds for converging direct payments to farmers across the EU and for cutting cohesion and rural development funding for the country.
The president and the ambassadors also discussed migration issues. There have been tensions in the EU recently as countries disagree on how to curb illegal migrant flows.
Grybauskaitė called on the EU "to strengthen the protection of external borders, help countries outside the European Union from which illegal immigrants originate and speed up their return home", her office said.
"Lithuania has submitted a proposal on creating unified standards for the protection of external borders and closing the existing loophole," it said.
The EU's cooperation with NATO was also discussed at the meeting.
"The president pointed out that the EU should bring additional value to NATO, where possible and without duplicating the Alliance, especially in dealing with problems of military mobility, countering cyber and hybrid threats," according to the press release.
In a Lithuania-led initiative, six EU member countries earlier this week agreed to create European cyber rapid response teams.
The president's office noted that "Lithuania is also actively engaged in the Netherlands-led PESCO military mobility project, which should receive 430 million euros from the new multiannual framework to remove all barriers hampering the mobility of military forces and equipment".
Military mobility projects include the adaptation of civilian infrastructure, such as railways, roads or overpasses, for military use.
The president met with the ambassadors ahead of the EU summit on Thursday and Friday.