The commonwealth has opened the door to funding the Melbourne Metro Rail in an apparent thawing after months of hostility.

Federal Infrastructure Minister Warren Truss said he expected his government would be approached to fund one of the state government's key infrastructure projects, an $11 billion rail tunnel connecting north and south suburban lines through a second CBD subway.

The state government says 44 buildings covered by 94 property titles will be acquired to make way for the new metro line. Credit:Penny Stephens

"We will probably receive approaches in relation to that project," he said. "If we receive those approaches then we will have them assessed by Infrastructure Australia and make a decision."

His comments are at odds with Prime Minister Tony Abbott's resistance to funding Melbourne Metro. Mr Abbott has repeatedly insisted the federal government is opposed to funding urban rail projects.