President Jacob Zuma's second reshuffle of his Cabinet without consulting the African National Congress's (ANC's) top six is likely to deepen fractured relations within the party leadership and further threaten the relationship with the tripartite alliance partners.

"The ANC top six was informed," party secretary general Gwede Mantashe said on Tuesday when asked if Zuma had consulted them.

While the country’s constitution gives the president the prerogative to reshuffle his Cabinet, the ANC expects him to consult with its leadership and alliance partners.

While Mantashe refused to go into details of the meeting with Zuma when he informed them of his plans, his comments indicated that there was disapproval.

"The ANC can have a particular view on a matter, but if the president invokes his prerogative as given by the country’s Constitution, as ANC, we have little space to manoeuvre," Mantashe said.

Mantashe was speaking at ANC headquarters in Luthuli House during a scheduled interaction with journalists about an hour after the Presidency announced the reshuffle.

He said it was a "pity" that Blade Nzimande, who is also the general secretary of the South African Communist Party (SACP), had been removed as minister of higher education and training.

"He has done well in education. Under his leadership, he has built three universities. We hope he won’t resign from Parliament and will stay there and have his energy used there," Mantashe said.

Mantashe was surprisingly frank on the "negative impact" the move would have on relations with their alliance partners.

The relationship with the SACP is already at an all-time low.

Tensions within alliance

"We just had an alliance secretariat meeting after six months to try put it [back] together again.  [The] reshuffling of GS [general secretary] of the SACP is going to undo the work done by the secretarial meeting. But it is not about individuals. We must invest in sustaining the alliance all the time," he said.

Relations with the SACP and trade union federation Cosatu soured after Zuma axed Pravin Gordhan as finance minister during his midnight reshuffle at the end of March, without consulting them.

The SACP publicly discussed the content of their meeting with Zuma, telling the media that the president had fired Gordhan over a "dodgy" intelligence report.

The party has become one of his biggest critics over state capture and has since called for Zuma to step down. He has also been banned from speaking at SACP events.

Mantashe also criticised Zuma for changing the portfolios of three ministers, just less than seven months of appointing them during that March reshuffle.

"For us, the more you keep political leaders at portfolios for a long time, it allows people to understand the portfolio and stabilise them. If there is quick turnover, it will impact on stability of portfolio and government," he said.