Treasury secretary Jenny Wilkinson has conceded Labor’s capital gains tax changes won’t be a simple reversion to the system that existed before 1999 as Anthony Albanese claimed in Parliament.

The new changes passed through the lower house after a series of 21 votes – designed by the Opposition so they could claim Labor voted against larger tax cuts – that dragged on for more than four hours on Thursday.

But their route through the Senate is looking tougher with the Greens raising concerns there’s a “secret backdoor” that allows the Treasurer to water down what the minor party already views as weak measures.

Opposition Leader Angus Taylor is open to working with the Greens to block the tax package, despite his belief that the changes are too harsh rather than too weak.

The Government wants to replace the 50 per cent capital gains tax discount with one based on inflation and limit negative gearing to new builds.

The legislation also creates a $250 annual working Australian tax offset and a $1000 standard deduction.

The Prime Minister last week told the House of Representatives that Labor’s plans for the capital gains tax discount reinstated the indexation model that had been in place from 1985 to 1999.

“We are also changing the capital gains tax regime to go back to 1999,” he said.

Under questioning from shadow finance minister Claire Chandler on Thursday, Ms Wilkinson admitted Labor’s Budget plan didn’t include the pre-September 1999 model of allowing income to be averaged out over five years.

“That has not been part of the announcements that the Government’s made in relation to the tax package”, she told an estimates committee.

Ms Wilkinson also confirmed the capital gains regime from 1985 to 1999 did not put a minimum 30 per cent impost on the taxable portion, as Labor is proposing to introduce from July 2027.

Finance Minister Katy Gallagher answered a question directed to Ms Wilkinson to argue that Mr Albanese was simply outlining Labor’s capital gains tax changes would include a return to indexation.

“I think the PM was relating comments there, were relating to the indexation model approach that was there in pre-1999,” Senator Gallagher said.

Mr Albanese was pressed during Question Time about the Treasury secretary’s contradiction.

“What we’ve moved from is a discount of 50 per cent to the discount system that was in place prior to 1999, which was a discount system based upon real gains. That was what was in place. That is the fundamental difference between the two distinctions,” he said.

Mr Taylor and shadow treasurer Tim Wilson accused the Government of voting against tax cuts 11 times, based on the tactical manoeuvring over the process to pass the legislation.

“Will the Prime Minister be up front with Australians and admit his government voted to steal hundreds of billions of dollars in extra taxes from hard-working Australians?” he asked.

The Coalition’s policy is to automatically index income tax thresholds, to eliminate bracket creep.

It tacked on a second-reading amendment – a procedural motion that doesn’t actually change the legislation – calling on the government to pass laws to end bracket creep.

It also sought to remove the capital gains tax and negative gearing changes from the legislation.

Both efforts were defeated given Labor’s massive majority.

After 16 hours of debate in the lower house over Tuesday and Wednesday, the legislation will now be scrutinised in a two-week Senate inquiry, which is holding hearings on June 15 and 16.

But the Government will have to win support from the Greens to get the laws through the Senate, which Treasurer Jim Chalmers said he wants done by July 2.

The minor party on Thursday aired concerns about the number of details that will be left to Dr Chalmers to fill in via regulation rather than being spelled out in legislation.

David Shoebridge labelled them “godlike” and “Henry VIII powers” and said the legislation as it stands “needs a really bloody close look at it”.

“It’s a real issue for us that the government has put a secret backdoor in their legislation to literally undermine any of the very minor changes that they’re putting to tax wealth,” he said.

The Greens are concerned that this follows an increasing trend from the Government to avoid parliamentary scrutiny, pointing to similar use of regulation for the 5 per cent deposit scheme, GP bulk-billing incentives and a crackdown on supermarket price gouging.

Dr Chalmers said he was aware of the Greens’ concerns, but he claims it’s not an unusual way to approach tax laws.

“Nobody has the numbers in the Senate on their own, and so we’re in those discussions with the Greens,” he said.

“As I understand it, they intend to raise it at the Senate committee over the course of the next couple of weeks, and that’s appropriate as well.”

Mr Taylor said he would “work with anyone to stop toxic taxes”, including trying to convince the Greens to split the bill.

“The question is whether there’s going to be a dirty deal done here between Labor and the Greens,” he said.

“The Greens have an opportunity here, though, to stop this legislation and we’ll work with whoever we can to stop this toxic legislation getting through the Parliament.”

Ms Wilkinson also conceded the negative gearing and capital gains tax changes would mean 35,000 fewer homes and admitted forecasts of $2 a week more expensive rent ignored the effects of investors selling properties.

In another awkward moment, she struggled to explain to shadow housing minister Andrew Bragg if a granny flat would be considered a new build, taking 26 seconds to flick through Treasury papers.

“Table two in the explainer, it says that a granny flat built adjacent to an established property that is not eligible for negative gearing is not an eligible new build,” she said.

The Coalition followed up with House Minister Clare O’Neil during Question Time, who said it was very clear what did and did not count as a new build.

“A granny flat built adjacent to an existing property – that isn’t eligible for negative gearing.

It’s actually in the Budget papers, which hopefully those opposite have managed to familiarise themselves with,” she said.