ANC secretary general Gwede Mantashe said although the NEC did not discuss the public protector's damning "State of Capture" report at the weekend, the meeting agreed that President Jacob Zuma establish the inquiry to look into allegations of state capture after the dawn of democracy.
"The terms of reference of such commission of inquiry must be broad enough to uncover the influence of business on the State," Mantashe told reporters in Johannesburg.
"The state capture issue goes further deeper than what is in the public protector report. The NEC agreed that the inquiry should start beyond 1994, and questions were raised whether it should also probe the 1948 era...It was agreed that a separate inquiry can be established for that period if the need arises."
Last week, Zuma's office denied reports that he was against the implementation of the public protector's remedial actions, including establishment of a commission of inquiry.
The Presidency said Zuma was of the view that some of the remedial actions directed were irregular, unlawful and unconstitutional.
"Legal advice obtained pointed at the fact that the remedial action on the appointment of a commission of inquiry undermines the separation of powers doctrine. The Constitution gives the power to appoint a commission of inquiry to the President, which she/he must exercise when the President holds a view that a matter of public concern requires such a process," Zuma's office said at the time.
The weekend NEC meeting, the highest decision making body in the governing party, saw Zuma survive a second attempt to force him to step down.
A defiant Zuma, backed by his supporters, reportedly told the NEC that the branches of the ANC elected him and that only they could remove him.
The motion against Zuma was tabled by the ANC's policy guru, Joel Netshitenzhe, on Saturday.
The move was supported by Health Minister Aaron Motsoaledi and his deputy Joe Phaahla, axed tourism minister Derek Hanekom and NEC member Sue van der Merwe, according to sources.
At an ANC NEC meeting in December, Hanekom, since dismissed by Zuma from Cabinet, proposed a motion of no confidence in him, but that, too, was squashed.
Mantashe said the NEC saw the calls for Zuma to vacate office as not about Zuma, but an attempt to "dislodge the ANC", a charge he said was led by opposition parties.
The NEC agreed that mistakes by the ANC should be minimised and reduced so that the opposition parties did not use such to their advantage, said Mantashe.
The NEC meeting took place against the backdrop of the most damning newspaper reports yet against Zuma's controversial friends, the Gupta family, revealing the business family's influence on the state allegedly through Zuma and his son Duduzane.
According to Sunday newspaper reports, Zuma and the wealthy family had come up with an exit plan for the President and his family to settle in the United Arab Emirates (UAE).