In a statement, the regulator says that Martas Martisius, the deputy chairman, will take over the role on a temporary basis.
The local media, including Delfi, say that Vaitekunas cited his lack of fluency in foreign languages as the reason for his decision to step down from the role.
However, he also admitted that it was due to the findings of the Committee of National Security and Defence (NSGK) into unlawful influence on political processes.
This included attempts by MG Baltic to gain influence on the LRTK, something that he has denied.
Broadband TV News notes that MG Baltic Media Group’s portfolio includes LNK, the most popular TV channel in Lithuania.