Zuma, who has himself been at the centre of several major corruption scandals, called on the African National Congress (ANC) to reform and turn around its fortunes ahead of elections in 2019.
Zuma may stay on as national president until the election, but he is due to step down as ANC chief in December and the party faces a bitter internal leadership battle.
He said that the ANC needed to "cleanse itself" of "corruption, social distance, factionalism (and) abuse of power".
Critics accuse Zuma, 75, of allowing corruption to flourish since he came to power in 2009, and of being in the sway of the Gupta business family, allegedly granting them lucrative government contracts.
The president has been admonished by the country's highest court, and is fighting a judicial order that could reinstate almost 800 corruption charges against him over an arms deal in the 1990s.
"Access to state power and resources has led to perceptions and allegations that the ANC is a corrupt organisation," Zuma said, vowing to fight against graft.
Zuma is seen as favouring his ex-wife, former African Union chief Nkosazana Dlamini-Zuma, to succeed him -- rather than deputy president Cyril Ramaphosa.
Dlamini-Zuma sat directly behind the president, in full view of the television cameras, while Ramaphosa was loudly cheered when he arrived on the stage.
The clash between the two camps could provoke further political instability in South Africa, which this month slipped into recession and also is suffering record unemployment.
Ramaphosa, a wealthy former businessman and trade union leader, has remained largely loyal to Zuma but sharply criticised him after the sacking of the respected finance minister Pravin Gordhan in March.
The president admitted that economic growth was lower than expected and that local elections last year had been a "serious setback" for the ANC, when it lost about eight percent of its previous national support.
He blamed the fall in support on perceptions that "we are soft on corruption, we are self-serving and that the ANC is arrogant".
Some veterans of the struggle against apartheid rule, which ended in 1994, boycotted the conference, which ends on Wednesday.
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