She said she would touch on this matter during her budget vote address.
She said Parliament is concerned about the plethora of cases against it by opposition parties and she accused these parties of being quick to run to the courts to resolve political disputes.
“This business of taking Parliamentary issues, including details of internal arrangements to court is not good for us,” said Mbete.
She said the opposition could run to the courts because they had money.
In the four previous Parliaments this did not happen, despite the fact that the ANC always had a majority, she said.
But in the current Parliament the opposition was quick to turn to the courts to resolve political disputes. She said a mechanism would have to be found to resolve this issue.
She said last year a meeting had been set up with three arms of the state in Cape Town to discuss judicial overreach.
But the matter had not been finalised as they still have to meet again.
The question of the separation of powers is important in the democratic dispensation, said Mbete, adding that she hoped the matter would be resolved soon.
In her briefing, she appeared to leave the door open to a Commission of Inquiry into state capture. Such an inquiry would help resolve many questions in the country, she said.
But she added that she had received a request from the DA for her to set up another inquiry into state capture. Neither had the portfolio committee on public enterprises asked her to set up an inquiry into Eskom.
The Guptas and President Jacob Zuma are at the centre of accusations on the capture of the state.
Mbete set up an inquiry into the SABC late last year, which fingered many senior officials in wrongdoing at the public broadcaster.
Deputy Speaker Lechesa Tsenoli said they have not received a letter by the DA to establish such an inquiry.
“The letter that has been written by the DA has not reached Parliament,” said Tsenoli.
Opposition parties had complained that they go to court because Parliament fails to hear them and implements its own decisions.
They run to the courts because there is nowhere else to go to resolve a stalemate.
Parliament has faced more than a dozen cases in court over the last three years.