Labour and Conservative councillors have joined forces to demand that the decision - made by the council's executive board on May 22 - be examined by a special scrutiny committee.
Education secretary Michael Gove and officials from the Department for Education (DFE) have also been requested to attend the meeting on June 13.
Scrutiny committee chairman Cllr Paul Bretherton said: "Committee members will now have the opportunity to consider the merits of the 'call in' and question the decision makers in this process. We all need to establish whether it has been taken within the principles of good decision making."
The controversy centres on moves by a group of parents in the Padgate area - backed by the DFE - to set up The King's Free School in the buildings currently used by Woolston High School.
All parties on the borough council want to convert the high school buildings for special education needs and have approved plans to do so.
But the DFE was indicated it could use special powers to take over the high school for the new Free School unless the council makes alternative accommodation available.
As a result, the council has reluctantly agreed that empty classrooms at Bruche Primary School could be used temporarily by the Free School and that, subject to planning approval, land could be made available at Hillock Lane for permanent buildings for the Free School.
Education chief Cllr Colin Froggatt and Liberal Democrat leader Cllr Ian Marks have both accused the DFE of trying to "bully" the council over the issue.
Leading the "call in" Labour councillor Lottie Ladbury (pictured) said: "For over two years we have been working up plans to provide decent educational facilities for 200 of our most disabled children, but these plans now seem to be under threat by the pressure being put on the executive board by the DFE. who have effectively said, if we don't grant them planning permission they will take away the land we desperately need."
Cllr Ladbury said the DFE appeared to be forcing the council's hand and, as a result, there was inadequate consultation.
The call-in is supported by Conservative leader Cllr Paul Kennedy and education spokeswoman Cllr Sheila Woodyatt.
Cllr Kennedy said: "I am not opposed to Free Schools, but in this case it seems the council is acting under duress. Warrington has long-standing plans to use Woolston High School for Special Needs education which appear to be put in jeopardy.
"I do think the DFE need to be made aware of the special circumstances here in Warrington."
Woolston High is due to close at the end of summer term in July and the King's School - which is already advertising for staff - hopes to open in September.