Jones finished a poor third in the council elections on May 1, losing his Salford seat to Richard Houlton from the anti-congestion charging Community Action Party (CAP).
The elections will alter the make-up of the GMPTA from the top down. If Manchester's new councillors move against congestion charging, then the scheme is unlikely to get the go-ahead even if the Department for Transport (DfT) approves it.
Manchester is awaiting the DfT's verdict on its Transport Innovation Fund bid. This is intended to help fund the introduction of the congestion charging scheme.
If successful, Manchester could benefit from £3bn in transport investment, and would introduce a congestion charging scheme.
Failure to implement the congestion charging scheme would mean Manchester would miss out on the associated £3bn of TIF funding needed to upgrade the city's tram network.
NCE spoke to CAP leader Peter Franzen, who lost his Golborne & Lowton seat on May 1.
"Roger Jones losing his seat is a body blow for congestion charging in Manchester," he said.
Franzen claimed to have been a "thorn in the side," of congestion charging, and said the Labour Party "used their resources to unseat me, but they should have been helping Roger Jones instead," he said.
- NCEs Integrated Transport conference takes place on 10 July in London. Go to http://www.ncetransport.co.uk/ for more information.