He said he did not want to gate-crash "a private family funeral".
"Tutu will be travelling to Qunu early tomorrow morning to attend Tata Madiba's funeral," his spokesman Roger Friedman said later.
He gave no further details after a day of conflicting statements as to whether the former archbishop of Cape Town would be attending the funeral in Eastern Cape province.
Archbishop Tutu issued a statement earlier saying: "I would have loved to attend the service to say a final farewell to someone I loved and treasured."
However, a presidential spokesman insisted he was among those invited and any problems would be sorted out.
"The arch is not an ordinary church person; he is a special person in our country and he is definitely on the list," Mac Maharaj told AFP news agency.
"If there's any problem we will try to iron that out, but I can assure you that he is on the programme."
Government spokesman Collins Chabane also said that Mr Tutu was on the guest list.
The archbishop's office said he had cancelled plans to travel to the Eastern Cape for the burial after receiving no indication that he was invited.
"Had I or my office been informed that I would be welcome there is no way on earth that I would have missed it," the statement said.
Archbishop Tutu, a Nobel Peace Prize winner, was a friend of Nelson Mandela for decades.
He chaired South Africa's Truth and Reconciliation Commission, which investigated human rights abuses carried out during the apartheid era, and was a visible symbol of the anti-apartheid struggle during the decades of Mr Mandela's incarceration.
He has been critical of the current ANC government led by President Jacob Zuma.
The archbishop was not initially due to speak at Tuesday's memorial event for Mr Mandela in Johannesburg.
However, he was invited to the podium to say the closing prayer at the event and scolded the unruly crowd for booing Mr Zuma.