Labor and the Greens have joined forces to vote down the abolition of the CEFC.
The government will reintroduce the bill to abolish the CEFC next week.
Federal Treasurer Joe Hockey said the government had gone into the 2013 federal election with a plan to abolish the carbon tax and the CEFC.
Its bid to abolish the carbon tax earlier this year also failed with the senate also blocking that plan.
The bill to abolish the carbon tax will also be put to the new senate that comes into effect from July 1.
In a joint statement Hockey and Finance Minister Mathias Cormann said the Australian people had decided, at the federal election past, that they wanted the CEFC abolished.
“This mandate has now been ignored by Labor and the Greens twice,” the statement said.
“The government does not believe it is appropriate to keep borrowing money to underwrite a $A10 billion taxpayer funded bank that cherry picks investments in direct competition with the private sector.
“Australia does not have a good history with government owned banks.”