SACP leaders who serve in government will continue to do so but can be recalled any time the party feels they are not executing its mandate.
This decision was taken at the SACP's four-day congress held at the University of Limpopo at Mankweng, near Polokwane.
The decision came after questions were raised about positions held by SACP secretary-general Blade Nzimande - who is the Minister of Higher Education - and his deputy Jeremy Cronin - who is the deputy transport minister. On Thursday Nzimande said the party deployed its key members into government to ensure that commitments made in the ANC election manifesto were fulfilled.
He said the ANC election manifesto was as much part of the SACP as it was of the ANC. He said the party had to make sure it deployed cadres who would remain accountable to the party. He said previously members of the party joined government and then abandoned the SACP.
The party believes that President Jacob Zuma's takeover has created space for communists to operate, allowing differences to be discussed within the alliance.
Cosatu general secretary Zwelinzima Vavi warned delegates that SACP leaders should be held accountable to ensure that they were not "swallowed by the state".
Vavi said the state was "a massive monster", but also said SACP members must guard against a situation where the state could be used as a weapon to provide jobs for party leaders.
Nzimande has defended the dual positions situation, arguing that there had always been dual membership in the tripartite alliance, with communists being part of government since 1994.
The congress also resolved to strengthen the party by establishing 70000 branches by 2012.