Struggle veteran Ahmed Kathrada died early on Tuesday morning‚ his foundation said..
"They acknowledged the fact that the matter under investigation is also under judicial scrutiny in the Western Cape Division of the High Court," they said in a joint statement.
"In conclusion, the public protector and the minister committed their respective offices to work in a spirit of co-operative governance in line with the provisions of chapter three of the Constitution."
Public Protector Thuli Madonsela and Communications Minister Faith Muthambi met in Pretoria on Wednesday.
This was after Madonsela had subpoenaed Muthambi to appear before her in connection with her investigation into Motsoeneng's appointment.
The Western Cape High Court was currently hearing a bid by the Democratic Alliance to have Motsoeneng's appointment as chief operating officer set aside.
In February, Madonsela released a report on Motsoeneng, while he was acting COO. She found his salary increased from R1.5 million to R2.4m in one year, that he had purged senior staff, and misrepresented his matric qualifications to the SABC. Madonsela recommended that a new COO be appointed at the SABC within 90 days.
In July, Muthambi announced Motsoeneng's permanent appointment. She said he was cleared of all wrongdoing by a legal firm before the decision was made.
The DA then launched its high court bid.
In the joint statement on Wednesday, Madonsela and Muthambi said the meeting was "cordial, fruitful and informative".
"Both the minister and the public protector agreed on a way forward in addressing the matter as well as other issues of mutual concern," they said.