The committee says the 'online compliance system' lacked procedural fairness at every stage and had put thousands of innocent Australians through the trauma of having to prove they do not owe the money the welfare agency demanded.

In a report published on Wednesday evening, the Senate Standing Committee on Community Affairs, which has spent months investigating the controversy, recommended the program be stopped and overhauled "before more harm is done".

But two Coalition senators on the committee published their own report on Wednesday, dissenting from the view of the majority Labor-Greens members and rejecting their central conclusion that robo-debt lacked procedural fairness.

The minister in charge was quick to condemn the committee's work as factually inaccurate and politically motivated.

The debt program, that automatically matches information supplied to Centrelink with that given to the Tax office and raising debts when it detects overpayments, has been bitterly controversial since late 2016.

The committee wrote that between November 2016 and March 2017, at least 200,000 people were affected by the program with Centrelink sending out 20,000 letters, which it denies are demands for money, each week during that period.

Robo-debt sparked a storm of community, political and online protest and even before the report's publication on Wednesday evening, community and welfare groups including the St Vincent de Paul Society, Victorian Legal Aid and Anglicare Australia called for an end to the program.

Labor and activist group GetUp! were also calling for an end to the auto-debt recovery program on Wednesday.

The reference committee spent four months investigating, held nine public hearings, received 156 submissions and 1400 emails from the public and interviewed more than 140 witnesses.

The committee found that Centrelink had reversed the burden of proof onto its clients, forcing them to find paperwork going back years in many cases to prove they did not owe the money demanded.

There was also sharp criticism of the system for challenging the debts, poor communication and allegations of hardball tactics by private debt collectors being paid on commission by Centrelink.

"We heard time and time again of distressing tactics used by Centrelink and private debt collectors...in attempts to rake back potentially false debts," the committee's Chair, Greens Senator Rachel Siewert wrote.

"It seems in certain instances, getting the money back came above all else and was at the expense of the recipients mental wellbeing and financial stability."

The welfare agency's parent department, Human Services, did not respond on Wednesday evening to a request for comment.

The 21 committee recommendations, which are non-binding on the government, address the program's problem with calculating debt, communication problems, the charging of additional "collection" fees, difficulties challenging debts, and the "disturbing coercive tactics" used by debt collectors.

"Enough people have been hurt by this program which was designed to get money back quickly regardless of the impacts and whether it is legitimate debt," Senator Siewert said.

"Urgent action needs to be taken by the government before more harm is done".

In their dissenting report, Liberal senators Jonathon Duniam and Linda Reynolds acknowledged problems with robo-debt and there were more improvements to be made but said that Centrelink had worked hard to improve its systems.

Human Services Minister Alan Tudge went further on Wednesday night.

"This is a politically motivated and factually inaccurate report, reflecting the fact that Labor and the Greens don't support auditing of the welfare system," the minister said.