Former Greens senators Larissa Waters and Scott Ludlam could be on the hook for $3 million in parliamentary salaries – a debt their party leader thinks should be waived.

Richard Di Natale said Mr Ludlam and Ms Waters, who resigned from the Senate within days of each other after being found to be dual-citizens, and therefore ineligible to stand for Parliament under the constitution, had "already paid a pretty high price" and should not have to pay back money earned since their elections.

Mr Ludlam, who was elected in 2007, is estimated to have earned $1.6 million during his time in Parliament. Ms Waters, who won a Queensland Senate spot in 2011, is estimated to have earned $1.2 million before stepping down on Tuesday.

Senator Di Natale, still reeling from losing his two deputy co-leaders and scrambling to reassure a shocked and disappointed membership party processes will improve, said he believed Ms Waters and Mr Ludlam should receive the same treatment Special Minister of State Scott Ryan afforded former Family First senator Bob Day, and be granted a waiver.