A spokeswoman for the U.S. Attorney's Office in Utah said the decision was being reviewed and declined to comment.
Benson originally had sent MacKay to prison for 20 years based on a minimum mandatory sentence that was required because MacKay was convicted for causing the death of patient David Wirick, who died after taking two prescription drugs.
But since that conviction, the U.S. Supreme Court in a similar case held that controlled substances like the oxycodone and hydrocodone Mackay prescribed to Wirick must individually be capable of causing a death for a mandatory minimum sentence to be enacted.
Prosecution experts testified at the trial that the death likely came from a combination of drugs, while the defense asserted that pneumonia could have killed him.
Freed of having to impose a minimum of 20 years in prison, Benson said a sentence of three years was appropriate to reflect the seriousness of his conviction and to act as a deterrent to others.
The judge also cited MacKay's nearly two years in prison where he has been a "model inmate" who completed 22 educational courses and acted as a tutor to others.
MacKay, 66, also suffers from diabetes, coronary artery disease, hypertension, high cholesterol, obesity, gout and cirrhosis of the liver and has had numerous surgeries, Benson said.
MacKay has been serving his sentence at the low-security Terminal Island federal prison in San Pedro, Calif., according to the U.S. Bureau of Prisons.
He was indicted in August 2010 on 129 charges related to prescribing more than 1.9 million hydrocodone pills and nearly 1.6 million oxycodone pills between June 1, 2005, and Oct. 30, 2009, and accused of pushing 80 to 120 patients through his office in an eight-hour workday.