Speaking to the Minneapolis Star Tribune, officials investigating the artist’s death said the pills were labelled as hydrocodone, a weaker type of opioid.
Autopsy results released in June revealed Prince died of an accidental fentanyl overdose.
Officials told the Associated Press the singer had no prescriptions for controlled substances at the time.
Prince was found dead at 57 in an elevator inside his Paisley Park home in April.
According to the Star Tribune report, the musician weighed just 50kg (8 stone) at the time of his death and had significantly more than a fatal dose of fentanyl in his system.
Fentanyl has been linked to a surge in overdoses in parts of the US after being incorporated into counterfeit pills.
The counterfeit pills found in Paisley Park contained a variety of drugs, according to the Associated Press, including fentanyl, lidocaine and U-4770, a synthetic drug eight times more powerful than morphine.
Tests on Prince prior to his death did not show fentanyl in his system, AP said, citing an official involved with the investigation, indicating the singer was not a long-term user of the drug.
The official said Prince had many of these pills with him a week before his death when his airplane made an emergency stop in Illinois after he fell ill.
He reportedly received two doses of Narcan, an antidote used to reverse suspected opioid overdoses.
A singer, songwriter, arranger and multi-instrumentalist, Prince recorded more than 30 albums. His best known hits include Let’s Go Crazy and When Doves Cry.