Bosses want measures included in the Bill giving passengers seamless interchange between the proposed Birmingham Curzon Station and the existing Moor Street Station.
It is also calling for the Government to commit to having a fully segregated tunnel linking HS1 to HS2 to enable direct services from Birmingham to Europe without having to change between Euston and St Pancras.
The project is due to receive its second reading in Parliament in April.
Centro has announced it is set to lodge a formal appeal against the Bill in its current format – standard procedure in the early stages of such parliamentary legislation.
The authority – which comprises the leaders of the region's seven councils and decides on transport strategy in the West Midlands – insists it is strongly in favour of HS2.
But board spokesman and Wolverhampton City Council leader Councillor Roger Lawrence said Centro was using its right to raise concerns for passengers.
"We believe that HS2 must be built, indeed we believe it is vital for the future prosperity of the West Midlands," he said.
"However in order to get a better deal for passengers who will use HS2 and be able to argue our case at the Parliamentary Select Committee we have to formally launch a petition against the Bill in its present format.
"This is standard practice and will ensure we can make our case to seek changes that are important to Centro in the development of HS2."
Centro's concerns over the Bill in its present form are it will not deliver an efficient interchange facility between the new Birmingham Curzon station and the existing Moor Street station, it will affect plans to extend the Midland Metro in Eastside, and will affect the movement of traffic and pedestrians as a result of the closure of Park Street and the re-direction of traffic onto Moor Street Queensway.
It is also worried about a 'lack of integration' of the existing Birmingham International/NEC station with the proposed HS2 Interchange station.
Councillor Lawrence said Mr McLoughlin's decision last week to scrap a proposed single track link between HS1 and HS2 would remove the immediate prospect of direct high-speed services from the West Midlands to Paris, Brussels and beyond for the foreseeable future.
He said the Department for Transport and HS2 Ltd should make it clear that there will be such a link and that this will be implemented at the earliest possible opportunity.