Labor and the Greens have joined up with the crossbenchers in a bid to change the Federal Government's multinational tax laws.

The two parties have narrowly won a vote in the Senate, amending the legislation which would force private companies with an income of $100 million a year or more to publicly reveal tax and revenue information.

The original legislation passed through Parliament last month, which tightens the rules surrounding multi-national tax avoidance.

But it also allowed privately-held companies to publicly withhold information, following claims it would have exposed them to security threats.

The changes had not been formally locked in via Royal Assent, leaving the door open for a last minute change.

The Opposition and Greens have been able to bring on another vote, with additional amendments, following negotiations with crossbench Senators.

Under the changes, companies would have to specifically apply to the tax commissioner if they feared the publicly available information would prejudice commercial negotiations.

There would also be additional disclaimers published by ASIC about interpreting the published information.

The changes still need to pass through the Lower House before it becomes law.

It now puts the Federal Government in an awkward position over whether it will support the measures passed by the Senate or scrap the bill completely.

Assistant Treasurer Kelly O’Dwyer has criticised the move.

"These amendments will do nothing to increase the ATO’s powers," Ms O'Dwyer said in a statement.

"Labor and the Greens are clearly playing politics.

"The delay of the Multinational Tax Bill will stop increased penalties for multinationals who flout the law and don't pay their fair share of tax."