Scores of manufacturing jobs in Ballarat - which covers two of Victoria's most marginal seats - are under threat after a local train builder was quietly culled from the shortlist to make 25 new trains for Melbourne.

Two Asian rail giants remain in the bidding to build the trains, putting about 70 jobs in Ballarat under threat.

A Metro X'Trapolis train. Credit:Paul Rovere

Labor and transport experts have criticised the highly secretive tendering process - part of the multibillion dollar upgrade of the Cranbourne-Pakenham rail lines under a public-private partnership - for its lack of probity and for putting local jobs under threat.

Contracts are due to be signed by September 30 as the Napthine government races to lock in the project before the November election.