Prosecutors questioned the surgeon twice last week over operations carried out on 2011 and 2012, Dagens Nyheter reports.
“The suspicions concern crimes relating to the operations,” prosecutor Anders Tordai told the newspaper.
Previously an internationally renowned surgery star who operated on numerous Swedish and international celebrities, Macchiarini was sacked in March by Sweden's Karolinska Institute (KI) after growing controversy surrounding his medical methods.
The Italian attained world fame after completing the first synthetic trachea transplant using stem cells in 2011.
He made a name for himself in Sweden for three trachea operations at Karolinska University Hospital. But two of the patients died, while the third sustained serious injuries and remains in hospital in the United States.
KI first filed a complaint alleging that Macchiarini had downplayed the risks of the procedure in 2014 and suspended all synthetic trachea transplants shortly afterwards.
A previous article in the medical journal Läkartidningen described the Macchiarini case as an “ethical Chernobyl” for the institute.