On Saturday, Lendahl decided to step down as secretary general of the Nobel Assembly and the Nobel Committee in Physiology or Medicine at Stockholm's Karolinska Institute.
The Karolinska Institute University Board said it launched an external investigation into the hiring and work of Macchiarini who is a visiting professor at the facility.
Macchiarini had performed experimental transplants involving plastic windpipes coated with the patient's stem cells and has been accused by several colleagues of overstating his outcomes and the effectiveness of the procedures.
On Friday, Macchiarini was notified by the Institute's vice chancellor that his contract would not be extended.
Lendahl has not be accused of any wrongdoing but thought it best to step aside while the investigation was ongoing.
"As professor Lendahl anticipates that he may be involved in this investigation, he resigns from his position as Secretary General out of respect for the integrity of the Nobel Prize work," read a news release from the professor Rune Toftgård, chairman of the Nobel Assembly.
The assembly is an independent body of 50 professors from the Karolinska Institute which awards the Nobel Prize in Physiology or Medicine.