The Baird government's plans to create larger councils through its "Fit for the Future" amalgamation program is headed for a parliamentary inquiry which could delay or even derail the ambitious plans to merge 41 Sydney councils into about 18 by the end of the year.

Christian Democrat Paul Green has won support from the Greens and the Shooters for an upper house inquiry, which would not report until August 17.

Meanwhile councils have a deadline of June 30 to lodge their submissions with Independent Pricing and Regulatory Tribunal which will assess them. It will decide whether the councils are "fit" or "unfit" either as merged groups or as solo councils and had hoped to report by October 16.

Mr Green's inquiry specifically makes reference to the tight timeframe for councils to lodge their submissions, putting pressure on the government to halt the amalgamation process.