The retired judge heading the royal commission into antisemitism and the Bondi beach massacre warned the government that rules blocking access to sensitive secret information were “impeding” the work of her team, in particular the preparation of an interim report on security and intelligence failures due at the end of April.

The commissioner, Virginia Bell, relayed the message in a letter just days before the former spy chief Dennis Richardson, who was supposed to be critical to the interim report, abruptly resigned from the national inquiry.

Richardson said the absence of the protections was not a factor in his decision, instead insisting he had become “surplus to requirements” after his initial job was folded into the wider royal commission, and suggesting he quit because he was not able to make a meaningful contribution to that inquiry.

But the Coalition opposition has warned the royal commission, for which they strongly campaigned, would be “fatally damaged” without his input, urging the government to get him back onboard.

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Laws to plug the legislative gap passed the Senate on Thursday afternoon, seven weeks out from the 30 April deadline for the interim report. The legislation creates extra protections for people to provide sensitive intelligence information to the royal commission; presently existing laws had blocked that information being provided to a royal commission.

The federal government earlier this month drafted laws to allow the commission to access protected material and allow current and former commonwealth intelligence and law enforcement officers to engage with the inquiry.

In her submission to a parliamentary inquiry into the bill earlier this month, Bell said the absence of the protections was a roadblock to the commission’s work – in particular the interim report.

“The urgent progression of these amendments is necessary to support the Royal Commission’s work. The inability to access, or further delay in accessing, information currently protected by secrecy offences is impeding the Royal Commission’s work,” the submission said.

In its submission, the attorney general’s department said secrecy provisions have prevented “and continue to prevent or delay” the production of important sensitive material.

Richardson, a former senior public servant, was initially appointed to conduct a rapid departmental inquiry into the security and intelligence agencies in the wake of Australia’s worst-ever terrorist attack, which killed 15 people and injured dozens of others. His inquiry was later folded into the royal commission’s remit when Anthony Albanese bowed to public pressure and called a national probe.

Bell confirmed Richardson’s departure in a statement late on Wednesday, sparking a wave of speculation about the reasons and questions about what it meant for the task of uncovering any security or intelligence failures prior to the 14 December massacre.

Dennis Richardson said the absence of the protections was not a factor in his decision to resign from the royal commission, instead insisting he had become ‘surplus to requirements’ and suggesting he was not able to make a meaningful contribution to the wider royal commission. Photograph: Lukas Coch/AAP

In a series of media interviews on Thursday morning, Richardson said he effectively became a “highly paid researcher” after his report was incorporated into the royal commission.

“I was being way overpaid for what I was doing,” said Richardson, whose role commanded a daily rate of up to $5,000.

The prime minister and Bell had hailed Richardson as uniquely qualified for the role after a decades-long career in the public service that included leading Asio, the defence department, Department of Foreign Affairs and Trade and serving as Australia’s ambassador to the US.

Richardson confirmed he was not consulted before Albanese announced the royal commission on 8 January, although he said the decision to merge his inquiry into it was “perfectly appropriate”.

He was confident the inquiry would be able to uncover answers without him, citing the body of work already completed and the quality of Bell and her team.

The royal commission was bound to confront legal and logistical challenges given the sensitives that surround the security and intelligence agencies and the need to avoid prejudicing the criminal trial.

Major Jewish groups in Australia, who had called for a royal commission into antisemitism and the Bondi attack, declined to comment on the change.

The Treasurer, Jim Chalmers, said he was sad to hear about Richardson standing down, but declined to comment on how it could impact the inquiry.

“Ultimately, it’s a matter for Dennis and for the royal commission, and hopefully we’ve been able to tap some of that considerable knowledge before this development today,” he said on Sky News.

The opposition seized on the news to claim the inquiry would lose credibility without Richardson’s help.

Shadow defence minister James Paterson demanded Albanese urge Richardson to reverse his decision and stay on with the inquiry, claiming it would be “fatally damaged” without the former Asio boss’ involvement. Shadow industry minister Andrew Hastie said he was “troubled” by Richardson’s announcement, claiming his departure would “delegitimise” the royal commission process.

“Dennis Richardson is uniquely qualified to interrogate and examine those questions, and so his departure, I think, poses questions about the legitimacy of the findings of the royal commission,” he told 2GB radio.

Opposition leader Angus Taylor raised concerns about the effect Richardson’s departure would have on the royal commission.

“To not have him as part of that team is a major, very serious loss,” he told a press conference.