They are alleged to have taken bribes to issue financial rulings in favour of the Camorra, the crime syndicate active around the southern city.
Altogether about 60 people are being held on suspicion of money laundering and corruption.
Buildings, cars and property worth 1bn euros (£829m; $1.3bn) were seized around Naples and in northern Italy.
The names of the detained 16 judges have not been revealed.
The police said the focus of the operation was the Fabroccino clan, which is believed to have bribed officials to obtain favourable court judgements.
The clan has become notorious for extortion and drug trafficking, but the police say they are also investigating its involvement in buying and selling property, hotel management and the food industry.
The authorities clearly believe that the corruption has spread far beyond the members of the clan itself, and that in this case even judges may have been working with the Camorra, the BBC’s Alan Johnston in Rome reports.
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