Lendahl resigned as secretary general of the Nobel Assembly, an independent body of 50 professors from the Karolinska Institute which awards the Nobel Prize in Physiology or Medicine, on Saturday.
He also chose to resign as a member of the Board of the Nobel Foundation, which manages the Nobel assets, ahead of an investigation into the Karolinska Institute's recruitment of Macchiarini
Lendahl has not himself been accused of wrongdoing.
"As Professor Lendahl anticipates that he may be involved in this investigation, he has resigned from his position as Secretary General out of respect for the integrity of the Nobel Prize work," Rune Toftgard, chairman of the Nobel Assembly, said in a statement.
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The surgeon performed experimental transplants involving plastic windpipes coated with the patient's stem cells and has been accused by several colleagues of overstating the effectiveness of the procedures.
Two of the three patients he operated on in Stockholm died, and a third has been hospitalized for more than three years.
An external investigation by the Karolinska Institute University Board is looking into the hiring and work of Macchiarini.
Last week, the Stockholm-based institute announced Macchiarini would not have his contract extended and his lab would be closed.