Final results confirmed that neither Netanyahu's bloc nor the Jewish opposition had won a majority in parliament. Meanwhile, Netanyahu's Likud accused Israel's Arab-led parties of stealing the election amid ongoing attacks on Arab voters and parties.
Eisenkot and every member of his bloc bar one has previously refused to enter government with Arab parties, but speculation has swirled in recent days that an agreement could yet be reached.
Eisenkot, who was briefed on the investigation, said it is too early to determine what happened, or if anything happened at all.
Israeli media reported that the CEC had been presented with a claim that Qatar had provided funding aimed at increasing voter turnout in Arab communities.
For years, many boycotted Israeli elections, saying voting would legitimise a system that they say treats them as second-class citizens.
Netanyahu's attacks on Arab voters and parties have been ongoing for days.
Netanyahu's bloc leading Israel election but short of majority, partial results show.
Netanyahu's Likud accused Israel's Arab-led parties of"stealing"the election.