It is understood around 20 redundancies are now planned before Christmas at the offices, which will be closed once existing projects are finished.
According to sources both offices have been letting staff go over several months but the latest wave of redundancies has distilled plans for a complete wind-down.
Future business development and pre-construction in the regions will be handled from the Bristol and London offices.
A spokesperson for Bouygues UK said: “Owing to a challenging market in the North and Midlands, we have decided to merge the Manchester and Birmingham operations of Bouygues UK with our offices in the South West and Wales.
“This will happen over time and existing projects in the Midlands and North West will continue unaffected through to completion.”
The Manchester office is understood to presently have one major project on the go with Birmingham working on two projects.
The company said that the Bristol and London offices would continue to target selected projects in these regions with repeat customers where Bouygues saw it could add value.
The spokesperson added: “We are consulting with staff affected and will look to redeploy them to other roles where possible.”
The firm emphasised that other Bouygues Group companies based in the North and Midlands were unaffected by the decision and would continue to operate as normal.
Bouygues Energies & Services continues to operate from One Didsbury Point 2 in Manchester.