"I can indeed confirm that he has resigned. I have received a text message from him in which he details reasons for his resignation," said regional secretary Zandisile Qupe.
He said Faku's resignation came as a surprise.
"I am surprised, but I can state that his resignation does not imply that he is cutting ties with the ANC permanently. He is a good leader and is well known in the community," Qupe said.
"The organisation will rely on his capabilities and experience from time to time."
Qupe said Faku indicated in the sms that he was resigning in order to take care of his business fulltime.
When contacted for comment, Faku said the matter was an internal one and would not discuss it further.
Faku, a former mayor of the metro, was re-elected chairperson of the Nelson Mandela region in April last year.
He was challenged by the city's mayor Zanoxolo Wayile.
Tensions between the two had reportedly become so strained last year that factions supporting both men came to violent blows forcing party bosses to step in.
In August, there were reports that Wayile was held hostage inside the ANC's Port Elizabeth offices.
Faku denied this saying the "story is a fabrication".
In September Faku and Wayile said they had buried the hatchet and agreed to work together going forward.
This was after Faku was quoted saying he would never back down in his quest to have Wayile and his team removed because they were "incompetent".
Faku came under fire in 2011 after he reportedly incited about 100 people at an election victory party and called for the regional newspaper, the Herald to be burnt down.
"The Herald dictated that DA leader Helen Zille , and Cope's Smuts Ngonyama would run the metro," Faku was quoted as saying at the time. – Sapa.