South African President Jacob Zuma will miss the United Nations (UN) general assembly in September in favour of attending the African National Congress's (ANC's) National General Council meeting (NGC), the Sunday Independent reported on Sunday.

The Presidency has confirmed that Zuma would send a senior government delegation to the meeting in New York, as the NGC "comes first", the paper quoted the Presidential spokesperson Zizi Kodwa as saying.

"When the date of the NGC was formalised, we were alerted to the overlap... We said we can't consider organisational issues (as) less (important) than anything. The NGC is the biggest political school of the ANC... the President will have to come," said Kodwa.

He said that the UN meeting would be attended by a "high senior delegation".

The UN general assembly will start on September 23 and Zuma was scheduled to address the gathering on September 25.

The ANC's NGC - a mid-term assembly to review party programmes - will take place from September 20 to 24.

The paper reported Kodwa as saying that Zuma's decision to stay and attend the NGC had nothing to do with suggestions of a planned revolt within the ANC.

This would be the second time since 1994 that South Africa would not be represented at the general assembly by a Head of State because of party politics, the paper said.

The first time was in 2008 when former President Thabo Mbeki was "recalled" by the ANC.