President Hasan Gerceker of the Court of Appeals branded that the arrangements regarding jurisdiction in the Constitutional amendment package "unconstitutional".
The AK Party says the changes are needed to curb the powers of an entrenched judiciary and to bring Turkey closer to democratic norms needed to support the country's bid for EU membership.
Gerceker held a press conference on Monday regarding the Constitutional amendment package which was prepared the government and envisages amendments to 22 articles of the Constitution, Anadolu news agency said.
Another senior judge said the proposals "were not the answer to the problems of the judiciary."
"They are fooling around with the high court," said Kadir Ozbek, head of the Supreme Board of Judges and Prosecutors (HSYK), which appoints senior members of courts.
The government wants to change both the composition of the HSYK and change the way judges are appointed.
It also wants to make it harder to ban political parties, and pass responsibility to the president for appointing most of the Constitutional Court's judges.
The EU has criticised Turkey's political parties law, under which almost 20 parties have been banned since the constitution was adopted in 1982 following a coup.
The AK Party itself narrowly survived a court attempt in 2008 to close it down on the grounds that it contravened the country's secular constitution.
"The government should avoid actions that could damage the principles of separation of powers and independence of the judiciary," Judge Gerceker said.
Gerceker singled out for criticism a proposed amendment that would make it harder to close down political parties.
He said making any decision to ban a party dependent on parliamentary approval was contrary to the principle of seperation of powers.
"We sense that the constitutional package is aimed at decreasing the power of the judiciary. We are definitely objecting to this," Gerceker said.
The government also aims to curb the influence of the once-untouchable military, which along with the judiciary is a stronghold of secularism.
The proposals include a measure to allow military personnel to be put on trial in civilian courts for crimes committed against the security of the state and the constitutional order.
Dozens of officers, including retired and serving generals, have been charged in civilian courts in recent weeks in connection to alleged plots to unseat the AK government.
The government also proposed an amendment to strip leaders of the 1980 military coup of their immunity from prosecution.
The AK Party, which first swept to power in 2002 ending the secularists' decades-old grip, has enough votes in the 550-seat parliament to pass a bill calling for a referendum.
Earlier in the day, a delegation of the ruling Justice & Development (AK) Party --formed by Turkish State Minister & Deputy Prime Minister Cemil Cicek, Justice Minister Sadullah Ergin and Deputy Group Chairman Bekir Bozdag-- paid visits to the Republican People's Party (CHP), the Peace and Democracy Party (BDP) and the Nationalist Movement Party (MHP) about the constitutional amendment package.
Top Turkish judges attack govt reform package
The AK Party says the changes are needed to curb the powers of an entrenched judiciary.