Labor plans to double the concessional tax rate on the proportion of superannuation balances above that level, to 30 per cent.
The policy was formulated after Treasury noticed a small number of people appeared to be using the system as a tax reduction strategy rather than solely for their retirement, as intended.
An aspect of the policy, to tax unrealised capital gains on those very large accounts, has proven contentious. Many are set up under self-managed super fund structures.
Unrealised gains are 'paper profits' - increases in the value of assets such as properties or shares that haven't been cashed in.
Treasurer Jim Chalmers has described the proposed change, first flagged more than two years ago and which is still before the Senate, as "modest".
"What this change is about, it's about making concessional treatment for people with very large superannuation balances still concessional but a little bit less so," he said last month.
"In terms of the calculation of unrealised gains, that's actually not unique in the system.
"And if you make a loss you can carry the loss forward."
Nationals senator Matt Canavan said taxing unrealised gains was a major sticking point for the coalition.
"There's no way in hell we'll support attacks on people that don't have the means to pay for it," he told Nine's Today show on Wednesday.
"This so-called tax on unrealised gains is incredibly unfair."
Tax on unrealised gains is already part of the Australian tax system and is, for example, paid under land tax regimes.
Greens Leader Larissa Waters told Nine her party, which holds the balance of power in the Senate, believes the threshold should apply to balances above $2 million, rather than $3 million.
"It's important to remember that I reckon nobody watching your show would be impacted by this tax," she said.
"It would touch only half a per cent of people - we are talking about folk who have an awful lot of money in their super accounts - that is not ordinary people."
On Tuesday, Prime Minister Anthony Albanese said that if the coalition was willing to negotiate a deal on the changes, then that was "good".
"I welcome the fact that they're saying that they won't just say no to everything from the very beginning but we'll, of course, talk to people in the Senate."
Mr Albanese noted that some super accounts are worth more than $100 million.
"That's not really to provide for an adequate retirement, is it?" he told Perth radio 6PR.
