A Federal Court decision to allow an overlapping native title bid for part of Western Australia's south-west has been described by one of the claimants as confusing.

The South-West Aboriginal Land and Sea Council is coordinating a joint Nyoongar native title claim over the entire south of the state.

But the Federal Court has ruled another group, the Harris Claim, could proceed with a bid for native title over the Busselton area, which is within the joint bid's boundaries.

Council chief executive Darryl Pearce says he would like clarification as to why the court is to allow two bids for the same area.

However, Mr Pearce says the joint Nyoongar bid will proceed, as either the decision will be appealed or the boundaries adjusted.

"Single Nyoongar claim is still going to be lodged, we may need to adjust our boundaries but definitely we are going ahead," he said.

"Those are our instructions from the Nyoongar community as a whole."