Roy Jobson told delegates that the city's recent inspection report was "unfair and unbalanced".
The report was published by the Office for Standards in Education before the date agreed with Manchester, and criticised its failure to find placements for 140 excluded pupils. It also highlighted Manchester's failure to issue all statements of special needs within six months.
Mr Jobson said councillors and officers accepted these findings, and were not "in denial".
"The main gripe we have is the lack of balance. Particularly in the OFSTED press release and in the commentary on the first few pages of the report, we felt it was unbalanced, unfair and something of a travesty," he said.
The authority responded to the first draft, on May 19, with 33 pages of commentary and corrections - and by last week had still to receive a reply.
The conference agreed a motion calling for publication dates to be agreed before inspection, and for reports to be presented in public to education authorities by representatives of OFSTED and its co-inspectors from the Audit Commission.
Mr Woodhead said the issue was "a festering sore that needs lancing", but upheld his right to publish reports early where serious problems were identified.
"We agree with education authorities a programme for inspection. That will include a date when the authority is to publish the report.
"In the case of some reports, however, the problems identified are of such magnitude and seriousness they need to be brought into the public domain sooner rather than later so solutions can be found," he said.