A temporary injunction was granted last week, amidst concerns construction would damage two sites that are culturally significant, according to a group of traditional owners from the Jagera people and the western division of the Wakka Wakka nation.
On Monday, the Land Court ruled against a bid to extend the injunction by native title claimant Adrian Beattie, allowing work to resume tomorrow morning.
Court mediation is set to take place on Wednesday, but Mr Beattie worries that may be too late to save the sites.
"They are going tomorrow, they're going to go straight through them," says the Wakka Wakka man.
Mr Beattie says there are bora rings and an ancient lookout at two separate sites on the proposed route.
"They're our churches, they're our school grounds - I put it in that context so that people can understand,
"There's only one other place that I know of on the (Darling) Downs that has these earthen ring features where the grass don't grow, and this one up here is pretty major."
The $1.6 billion bypass project, delivered by Nexus, will see the construction of a 41km road that will divert heavy traffic around Toowoomba.
Native title claimants from the Western Wakka Wakka peoples had previously given consent for the project to go ahead, but over a dozen traditional owners at Monday's hearing said they were never consulted.
The matter is due back in court on Thursday.