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The 64-year-old was accompanied on her flight by two doctors, who considered taking a defibrillator - a machine used to treat life-threatening heart conditions - with them on the plane, according to the report.
Mbete is expected to be back at work next week when Parliament's new term starts on August 19.
Parliament said Mbete was recovering well after being advised by doctors to rest and rebuild her strength following an intense election campaign in May.
According to the report, Mbete was well enough to walk aboard the jet, dressed in pyjamas and wrapped in a blanket.
She shared the plane with Defence Minister Nosiviwe Mapisa-Nqakula, who had to be dropped off in the Eastern Cape, before the plane continued with Mbete to Pretoria.
The flight took off on July 25, three days after Mbete delivered Parliament's budget speech in the National Assembly and two days after Mapisa-Nqakula delivered her budget speech, according to the report.
Mapisa-Nqakula's spokeswoman Joy Peter told the publication that the Ministerial Handbook allowed Mbete to use military facilities.
"Chapter 6 part 4 of the Ministerial Handbook clearly stipulates that members, which includes a Speaker of Parliament, may use SA Air Force aircraft for health reasons, and Ms Mbete was not well at the time," she was quoted as saying.