The call follows a study that found the present systems favour road building over alternative transport projects.
Buckinghamshire County Council joined with Friends of the Earth in a rare collaboration to commission an investigation into different options for improving transport in the area.
They wanted alternatives to the planned road building project called the A418 improvements.
“The road scheme has been proposed to solve some real local problems associated with traffic but this report shows it is not the best way to tackle those problems,” Stephen Joseph, executive director at Campaign for Better Transport, said.
“But the way in which the Government funds and evaluates transport projects means that the funding for the measures that will actually make a difference is hard to come by and justify.”
A DfT spokesman said: "The department's scheme appraisal system is highly regarded and widely supported.
The evidence base which underpins it was praised by the recent capability review and by Sir Rod Eddington, who noted its “world class” methodologies.
"However, we are not complacent and that is why we have recent launched a public consultation on how we might refresh our appraisal processes.
"The consultation period provides an opportunity for all individuals and groups affected by the guidance to engage with and participate in the process before changes occur during 2008."