Police said on Wednesday that they had to bore through a five-meter layer of reinforced concrete between Michele Zagaria's bunker and the floor of the house in which he was hiding.
The 53-year-old is the chief of the Casalesi clan of the Camorra, which controls a large territory in north of Naples.
In 2008, the clan's operations inspired a best-selling book titled Gomorrah: Italy's Other Mafia. The work was later turned into a prize-winning movie.
After arrest, Zagaria was sent to a high-security prison near the Novara town in northern Italy.
His bunker was about 50 square meters in area and hidden behind a thick wall opened and closed electronically. It was decorated with crucifixes and sacred images.
Before drilling their way into the bunker, the law enforcement agents cut off its electricity supply lines and blocked air supply to the hideout.