The party has confirmed that its top six met with Public Enterprises Minister Lynne Brown to discuss the matter that had heightened tensions within the party.
African National Congress spokesperson Zizi Kodwa said the party's leadership had "registered its discomfort" over Molefe's return.
"We can confirm the meeting took place yesterday [Monday] between the Minister of Public Enterprise with the ANC national officials, following the reappointment of Mr Brian Molefe," Kodwa said.
It is understood that some of the top six wanted Brown to reverse the decision, but Kodwa would only say that they had resolved that government must "deal" with it.
"The ANC registered its discomfort with this decision and the matter has been referred to government to deal with," Kodwa told News24.
Brown was summoned to Luthuli House on Monday after she announced that she had approved the board's decision for Molefe to return to the power utility as CEO.
This move has been seen as a defiance of the ANC.
Brown had earlier reversed the board's decision to give Molefe a R30m pay-out.
Molefe had resigned from Eskom after he was implicated in former Public Protector Thuli Madonsela's State of Capture report that investigated the "undue influence" of the Gupta family on executive decisions and in state-owned enterprises.
The ANC labelled the move "reckless and unfortunate", hours before Brown confirmed that she had approved Molefe's return.
"The decision therefore, to reinstate him in his former position, without these matters being resolved, is tone deaf to the South African public's absolute exasperation and anger at what seems to be government's lacklustre and lackadaisical approach to dealing decisively with corruption - perceived or real," the ANC said in a statement on Friday.
"The report, while still under review, made observations against Mr Molefe which, at the time, he had deemed serious and significant enough to warrant his resignation. Amongst others, he cited the interests of the company, good corporate governance and the interest of the public, as underlying his departure from the utility," the party said.
'Angered by actions of our deployees'
Molefe returns to Eskom following a short stint as a Member of Parliament.
At the time of his controversial move to Parliament, condemned by alliance partners SACP and Cosatu, there was speculation that President Jacob Zuma wanted to appoint him as finance minister.
However, during his April late night reshuffle, he appointed Malusi Gigaba instead, after the SACP and some in the top six voiced their disapproval of Molefe.
Last week, party policy expert Joel Netshitendzhe told delegates at ANC Northern Cape elective conference that the return of Molefe signalled that the party had lost control of its deployees.
"We are angered by actions of our deployees which demonstrate the vanguard has lost its DNA, its capacity to lead, let alone society, even to lead its own deployees," Netshitenzhe said to loud applause.