South African President Cyril Ramaphosa has removed the higher education minister from her position, his office said on Monday, after his party's key coalition partner accused her of misconduct.

The removal of Nobuhle Nkabane from her post could help defuse tensions between Ramaphosa's African National Congress (ANC) and the Democratic Alliance (DA), the two biggest parties in the coalition government, ahead of a budget vote this week.

The DA alleges that Nkabane helped engineer the appointment of ANC-connected individuals to the boards of skills development organisations and lied to parliament to cover that up.

Nkabane has denied the allegations against her, according to local television station eNCA. She said in a statement that it had been a privilege to serve in her position.

The DA welcomed Nkabane's dismissal. The party stepped up its criticism of the minister after Ramaphosa fired its deputy trade minister for not receiving presidential permission for an overseas trip, in the latest spat between the two main governing parties.

The DA threatened to vote against the budgets of departments led by ANC ministers it has accused of wrongdoing, including Nkabane, potentially disrupting the national budget.

Lawmakers are due to consider the last major piece of budget legislation, the Appropriation Bill, on Wednesday.