Science and Technology Minister Mosibudi Mangena will resign following the ANC's decision to oust President Thabo Mbeki, the Azanian People's Organisation said on Monday.

"After careful consideration of the position of Azapo's president in the cabinet, the standing committee has advised its president to resign with immediate effect," said Azapo secretary general Strike Thokoane.

Mangena is the leader of Azapo and the only non-ANC minister in the cabinet.

"Azapo has been following closely the unfolding developments around the decision by the NEC [national executive committee] of the ruling party to recall the president of the country," said Thokoane.

"It is the view of Azapo that this action leaves our country in a state of uncertainty and confusion, thereby leading to a crisis in government."

Azapo deputy president Pandelani Nefolovhodwe said Mangena had "accepted the advice [to resign]".

"He will be involved in the normal processes of resigning... he has accepted the advice," Nefolovhodwe told reporters in Johannesburg.

He said Azapo would not be influenced by African National Congress leaders calling for cabinet members to complete their office terms.

"We wouldn't really be guided by the advice of the ANC... we don't believe it [Mangena's resignation] will offend anybody."

Asked when his resignation would be tendered, Nefolovhodwe said the "resignation process" would start on Monday.

"I don't think it takes long to resign," he said.

Nefolovhodwe said Azapo rejected the notion that the "ANC will rule until Jesus Christ comes".

"Citizens must aim to change government from time to time... Azapo is going to campaign [ahead of general elections next year] to be the ruling party," he said.