The proposed legislation, seen by critics as a bid to head off a widening corruption probe that has rocked the government to its core, has come under fire from the domestic opposition as well as the European Union and the United States.
President Abdullah Gul has personally intervened to try to end the latest crisis to confront the government just weeks before the country goes to the polls in municipal elections in March.
Gul met Erdogan late today after holding separate talks on the divisive legislation with the leaders of the opposition Republican People's Party (CHP), the Nationalist Movement Party and the pro-Kurdish Peace and Democracy Party.
"This bill throws 90 years of democratic gains in the garbage," CHP leader Kemal Kilicdaroglu said after his meeting with Gul.
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"We want a judiciary which operates under the orders of conscience not a political authority."
Erdogan, who has dominated the Turkish political scene for more than a decade, has seen his grip on power shaken by the graft scandal which has targeted several key allies.
Erdogan has responded by conducting a mass purge of the police and seeking to push through the bill that would increase government control over the appointment of judges and prosecutors.
Turkey's top judicial body, the Supreme Board of Judges and Prosecutors (HSYK), has branded the measure unconstitutional.
A debate by parliament's justice commission on the bill descended into a brawl on Saturday, with politicians throwing punches, water bottles and even an iPad.
The United States and the European Union have both voiced concern over the measure, with EU enlargement commissioner Stefan Fuele calling for Ankara to ensure the proposals are in line with the principles of EU legislation.