The former Provisional IRA member formed the campaign group Survivors North West and has worked with victims of historical institutional abuse over the years.
A motion was passed last month to confer on him Derry City and Strabane District Council’s (DCSDC) highest honour.
However, unionist councillors at that meeting abstained from the vote.
On Thursday, a spokesperson for DCSDC confirmed that a call-in has been received over the decision to grant Mr McCourt the freedom of the city and district.
A call-in mechanism is an opportunity for elected members at council to ask that a decision that has not yet been implemented be looked at again.
A spokesperson for the council confirmed that the decision will be considered by members at September’s full council meeting.
People Before Profit councillor Shaun Harkin, who nominated Mr McCourt for the award, said he has now received notification of the call-in.
He said this was signed by both Ulster Unionist Party (UUP) and Democratic Unionist Party (DUP) councillors.
Cllr Harkin told BBC Radio Foyle: “It is obviously very disappointing.
“The call-in is also very surprising, given that both the UUP and DUP councillors present at that meeting abstained from the initial vote to award Jon the freedom of the city.”
In a statement, a spokesperson for the UUP confirmed their councillors have joined with other unionists on the council to call in the proposal to award Mr McCourt the freedom of the city.
“The UUP believes the process of civic awards by the council needs to be developed further and undertake to work with others to make this happen,” they said.
“To enable these discussions to take place we will make no further public comment until the council meets in September.”
Mr Harkin said there had been a great response from people following the announcement that Mr McCourt was to be awarded the honour.
He said he will be making the case again for him to be granted the honour in September.
Mr McCourt has worked with victims of Troubles-related violence and has been prominent in Derry’s Peace and Reconciliation group.
He spent more than two decades campaigning for an investigation into allegations of abuse in church and state-run institutions.
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