The bill, which Labor supported in the lower house, will be debated as early as Tuesday.

The government does not control the upper house, which means it is forced to rely on the conservative crossbench, including One Nation and the Shooters, Fishers and Farmers, to pass legislation.

"Labor have a very substantial bloc of votes [in the upper house] and they are taking advantage of that and putting union interests over community interests," Mr Constance said.

Key sticking points include the outsourcing of maintenance and privatisation, as well as employees on RMS awards not being forced on to Transport for NSW awards.

"Labor is just being led by the nose by the union leadership and completely undermining the intention of the bill in a completely destructive way," Mr Constance said.

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Labor's transport spokesman Chris Minns said the Opposition backed the merger but wanted to ensure that workers' rights were protected.

"Labor doesn't apologise for protecting jobs in regional NSW. We are on the side of the public when it comes to better transport coordination," Mr Minns said. "We support the merger. We are on the side of the workforce when it comes to making the government's commitments to them enforceable, including saving jobs in the bush."

Mr Minns said it should not be difficult to reach an agreement with the government.

"These are simple issues that should not be difficult. This is Andrew Constance's responsibility and he finds it difficult to complete the most basic of negotiations."

Mr Constance said the crossbench, including the Greens, had worked constructively with the government but Labor was "opposing the bill for the sake of opposing it".

He said the government would oppose Labor's amendments, which means the bill will need to return to the lower house.

Labor's roads spokesman John Graham said unions had been told that no legislation was required to merge the agencies only for a bill to be introduced days later.

"Because of that history, the government saying no legislation was required and then him [Mr Constance] turning up with legislation tucked under his arm, we say there is a need for transparency and a need to make sure that those provisions are subject to the closest scrutiny," Mr Graham said.