Previously an internationally renowned surgery star who operated on numerous Swedish and international celebrities, Macchiarini was sacked in March 2016 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 four trachea operations carried out on three patients at the Karolinska University Hospital. However, all three patients later died, one five years after the surgery.
Swedish prosecutors opened a criminal probe into the surgeries last year to investigate involuntary manslaughter or causing bodily harm, but announced on Thursday that they would not press charges.
"We have reached the conclusion that four of the five operations were negligently carried out, as the surgeon performed the operations using synthetic tracheas, which is in conflict with science and tried-and-tested practice," said public prosecutor Jennie Nordin.
"However, we have been unable to prove that any crimes have been committed. We cannot prove that the effects of his actions, with sufficient degree of probability, would not have occurred had another method been used," she said.
Prosecutors also cleared Macchiarini of causing bodily harm to a fourth individual, who suffered serious injuries after an operation using tried-and-tested methods in 2011.
"Regarding the fourth individual, we are not of the opinion that the surgeon's actions were negligent. Expert medical opinion is not unanimous regarding what should have been done instead for these seriously ill individuals, which therefore has made the suspicions difficult to prove," said Nordin in the public statement.
Macchiarini has denied all allegations, and his lawyer told the TT newswire on Thursday that "his opinion is that he did not act negligently and acted to help these people".
"He is of course happy and satisfied that it has been dropped," Björn Hurtig told TT.