The $150,000 cap was rammed into legislation after the Turnbull Government warned any push to lift it would delay the scheme's implementation by 18 months.

But the committee's unsuccessful attempts to solve the mystery has left survivors believing $150,000 was chosen because it matched Anglican and Catholic maximum payments, a joint select committee reviewing the scheme found.

"The committee is deeply dissatisfied that the maximum payment amount has been reduced and that no clear explanation has been provided about why this occurred or who advocated for this reduction," the report released on Wednesday said.

"The committee has tried to ascertain the reason for the reduction in the maximum payment and has put this question to various witnesses, including Department of Social Services and the Department of Human Services on numerous occasions. However, apart from acknowledging that $150,000 was the amount agreed to between the Commonwealth, states, and territories, the committee has not received any explanation or rationale about this discrepancy."

The committee, headed by Senator Derryn Hinch with Newcastle MP Sharon Claydon as deputy chair, was told more than 3000 people had applied for redress by February 28 after its launch on July 1, 2018, but only 88 cases were finalised, with fewer than 10 survivors paid between $100,000 and $150,000.

At least one person received the maximum $150,000.

"The committee recommends that the government clearly and openly explain how the maximum payments came to be set at $150,000 rather than $200,000, and the rationale for this decision," it said in one of 29 recommendations. The committee recommended amending legislation to lift the cap to $200,000.

The cross-party committee made up of four Liberal members, three Labor, one Green and Senator Hinch issued a damning assessment of parts of the redress scheme that vary from recommendations by the Royal Commission into Institutional Responses to Child Sexual Abuse in 2017.

They include an assessment matrix that restricts maximum payments to penetrative child sexual abuse, counselling capped at $5000 and excluding people with serious criminal convictions or making applications from jail.

The criminal conviction and jail exclusions would "disproportionately impact" Aboriginal and Torres Strait Islander peoples who made up almost one third of survivors seen by royal commissioners during private sessions in jail.

"This is an alarming statistic," the committee said.

Ms Claydon said the Federal Government's deviation from royal commission recommendations without sound evidence had been "to the detriment of the scheme and against the interests of survivors".

The committee accepted submissions from survivor groups, academics, lawyers and actuaries who called on the government to threaten the suspension of charitable status and tax concessions for institutions who failed to register with the scheme.

While institutions have until June, 2020 to register, and cannot register after that date, the committee accepted submissions arguing all institutions had been warned of the need to prepare since the royal commission released its national redress report in 2015 and urged its swift implementation.

The committee expressed concern there were no mechanisms to force private institutions to join the scheme, many institutions were yet to join and naming and shaming institutions had "not been sufficient".

"Plainly, more needs to be done to pressure non-participating institutions to join the scheme, and provide survivors with access to redress," the committee found.

"Institutions that refuse to recognise their role in the abuses that occurred and to accept responsibility for their actions should be subject to clear penalties, which could include the suspension of tax concessions and the withdrawal of their charitable status."

NSW Lawyers Alliance senior member Andrew Morrison, SC, said removing charitable status would leave institutions liable for council rates, land tax and Commonwealth income tax on earnings.

"For churches... the loss of their charitable status would be an enormously powerful incentive," Dr Morrison said.

The committee "agrees with the views express by Dr Morrison that non-participating institutions should not be able to retain their charitable status if they are not acting in the spirit of charity".  

"Institutions delaying their involvement until June 2020, in the committee's opinion, gives weight to the argument that they are just waiting for the problem to disappear as some survivors will die before that date," the report said.