Greens senator Sarah Hanson-Young said the minor party was concerned the proposed amendments bill, revealed on Tuesday by Finance and Public Service Minister Katy Gallagher, was being rushed through without detailed information, or consideration.

But Minister Gallagher said the case's implications could result in some lump sum super payments increasing by more than 10-times, adding it "doesn't pass the pub test".

A government motion on Wednesday morning to expedite the bill, which would retrospectively amend laws going back nearly four decades relating to Commonwealth superannuation benefits, was passed with bipartisan support despite the minor party's opposition.

A second reading was passed without amendments, leaving it all but certain to pass the Senate and go to the House of Representatives for a vote.

"That is not the type of parliament that the Prime Minister promised. It is not the type of collaborative nature that we continue to hear from all sides of how we are going to operate in this chamber," Senator Hanson-Young said.

"It is [a] deal being stitched up between the government and the opposition to effectively cut the wages of public servants - well, you can wear that but we are not going to be part of it.

"We are not going to be part of a bill being smashed through this place when we haven't even got answers to some basic questions."

Greens senator Barbara Pocock said the government's handling of the proposed changes was "very rushed" considering it posed a "complex" case.

"A rushed process, lacking a fullsome briefing, is problematic," she said.

The newly-elected Greens senator added she was concerned the amendments might change the Federal Court's ruling.

"We still don't understand the negative or unforeseen implications of the bill, [and] it seems will overturn possibly a court outcome and a case that's not yet been concluded," Senator Pocock said.

"It's important that government doesn't interfere with the courts and that we have a deliberate and clear separation of powers in what we're doing."

Minister Gallagher said the bill would allow the federal government to minimise the "significant windfall increases" in superannuation benefits that could be paid out following a Federal Court case court ruling.

The landmark court case, put forward by three department staff, argues superannuation payments are owed on rent-free housing provided by the government going back to 1986.

If the court rules in favour of the DFAT staff, it could set a precedent allowing thousands more to come forward and resulting in a bill reaching into the billions.

The Finance Minister, who also oversees the public service, said the changes were urgent to halt the potential of "widely variable and inequitable outcomes" for different employees.

Lump sum payments for some public servants, for example, could increase from $1.2 million to $11.7 million, she said.

"It doesn't pass the pub test," Minister Gallagher said.

"It's out of line with community expectations about the adequacy of superannuation arrangements and that is why we are dealing with this today."

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The Community and Public Sector Union responded sharply to Senator Gallagher's announcement on Tuesday, criticising it for "pulling the rug out" from under distressed public servants.

The union's deputy national secretary, Beth Vincent-Pietsch, said it is seeking an urgent briefing with the Finance Department to discuss the impact of proposed amendments.

"The payment of superannuation on rent-free housing has been a long and fraught issue for workers in areas of the APS," she said in a statement to The Canberra Times.

"It is very disappointing for those involved in the current Federal Court case, and those affected by the outcome, to have the new government change the goalposts in this way.

"Members affected by this superannuation issue are highly distressed by the government decision that pulls the rug out from under the case before the Federal Court."

Foreign Affairs Department staff Brendan Peace, Peter Fennell and Timothy Vistarini argued the Commonwealth did not pay them superannuation owed for a rent-free accommodation allowance they received on overseas postings and a "hardship" allowance as part of their salary on overseas postings.

The three public servants are fighting to include the allowances as part of their salary, which would result in additional superannuation payments being made available to their Public Sector Superannuation Scheme accounts on retirement.

The public servants' barrister, Lachlan Edwards, argued in April the senior officials, who had all worked within the public service for a number of years, had been provided with rent-free accommodation as part of their postings across cities considered "difficult".

The postings included Papa New Guinea's Port Moresby, Myanmar's Yangon and Solomon Islands' Honiara.