Attempts to link EduSolutions, the company contracted to deliver textbooks in Limpopo, to President Jacob Zuma's RDP Education Trust, were baseless and unfortunate, the Presidency said on Monday.
"Many companies donate to charitable organisations in South Africa, including the president's education trust," spokesperson Mac Maharaj said in a statement.
"Donors do not have any preferential treatment with regards to government tenders or any other state business."
Neither were they exempt from being investigated if the need arose.
"They are treated like any other company by government departments."
The contract between the Limpopo education department and EduSolutions was terminated after an investigation into the company by Treasury and other agencies started in December last year.
After the contract was terminated, new means for textbook delivery had to be sought, Maharaj said. He said Zuma had full confidence in the investigation.
Former Vlakplaas commander Dirk Coetzee was quoted in Sunday's City Press newspaper saying he personally introduced Zuma to EduSolutions founder Shaun Battlemann.
He said Battlemann "championed" Zuma's RDP Trust, and Battlemann visited Zuma at his estate in Nkandla.
Coetzee, who worked for the company as a security consultant, alleged textbooks were hidden in a warehouse instead of being delivered.
Battlemann also allegedly had a business relationship with a former education department director, guaranteeing him government contracts, and EduSolutions influenced education officials in various provinces.
In May this year, the High Court in Pretoria ruled the department's failure to provide textbooks to schools in Limpopo violated the Constitution. The application was brought by rights organisation Section 27.
Some pupils had been without textbooks for the past six months after the department failed to procure books on time.
The department was ordered to devise a catch-up plan to remedy the consequences of the delay, and to supply the affected schools with textbooks by 15 June.
The department failed to meet the court's deadline, but Basic Education Minister Angie Motshekga said her department met with Section 27 and agreed to move the deadline to June 27.
The minister said the department had accepted an offer from a company called UTI to help them deliver the books.
Former Higher Education director general Mary Metcalfe was appointed at the end of June to evaluate textbook deliveries to schools in Limpopo following the 27 June deadline.
Both the department and Section 27 agreed to appoint an independent person to verify claims.
Two more teams were set up on Wednesday to probe problems with textbook deliveries in the province. One was appointed by the presidency, the second by the Limpopo government.
Parliament's portfolio committee on basic education visited Limpopo on Thursday to gather information on the matter.
The national education department took over the running of Limpopo's education department in December following maladministration.