"We are not considering it yet. Time will show. The membership aspiration cannot simply be a goal in its own right," he said in an interview with the Lietuvos Žinios daily, published on Friday.
Asked about Azerbaijan's orientation towards the EU or Russia, the vice-minister said that "Southern Caucasus, especially Azerbaijan, has to be the center of a constructive dialogue between the West and Russia."
The Lithuanian-Azeri Intergovernmental Commission met in Vilnius this week.
Azerbaijan is part of the EU Eastern Partnership program. Diplomats say, however, that Azerbaijan is skeptical about the program and is seeking "a strategic partnership" with the EU.
Vilnius will host an Eastern Partnership summit in November under the Lithuanian EU presidency.