Berlusconi has been critical of magistrates - whom he accuses of being "communists" out to destroy him - for months and has vowed to overhaul the judiciary with reforms that critics say are tailor-made to shield him from prosecution.
In appeals court ceremonies marking the start of the judicial year, magistrates from Sicily to Milan walked out with copies of the constitution in hand when government representatives began their speeches.
Magistrates have been particularly incensed by a draft bill that would drastically cut the maximum duration of Italy's slow-moving trials, which would terminate two corruption and tax fraud trials against Berlusconi.
The prime minister denies all charges and says he is the victim of magistrates who hound him.
However, many magistrates agree reforms are needed.
The chief justice of the supreme court on Friday said Italian trials moved "slower than those in Gabon".
However, they also argue that an artificial time limit is counterproductive and may boost crime.
Government officials described the protest as lacking in credibility and urged magistrates to engage in dialogue instead.
"When criticism is blind and refuses to acknowledge anything, it is less credible," Angelino Alfano, the minister for justice, said during a ceremony in L'Aquila.
Berlusconi lost his immunity from prosecution in October when Italy's top court ruled that legislation passed by his government to shield him from trials while in office violated the constitutional principle that all are equal before the law.
That ruling allowed two court cases against him to resume.
Since then, the 73-year-old conservative leader has pledged a far-reaching overhaul of the legal system. He says that over the past 15 years he has been saddled with 109 trials and $280.8 million in legal fees, and was never convicted.