Under new powers passed by Parliament last week, federal police and organized crime investigators will be able to take over the online "dark web" accounts of criminals and terrorists and break into their networks.
But legal and human rights groups are concerned that the government has not taken on board all of the cross-party committee's recommendations, particularly the call for judicial oversight, and that the law was debated and passed in less than 24 hours.
The Australian Federal Police and the Australian Criminal Intelligence Commission will now have unprecedented powers to infiltrate criminal networks using domestic servers operating on the dark web. They will also be able to modify or remove harmful content, such as child abuse material, under the law.
The powers will be independently reviewed after three years, reviewed by Parliament after four years and end after five years, and provide stronger protections for journalists and third parties under changes made by the government in response to concerns raised by Parliament's powerful Intelligence and Security Committee.
Interior Minister Karen Andrews said she had adopted the committee's recommendations in good faith and that the amendments would ensure that arrest warrants are more likely to be issued for more serious types of crimes.
But she did not adopt a recommendation that the warrants should be approved by a federal court or Supreme Court judge, rather than by a member of the Administrative Appeals Tribunal. The Greens tried unsuccessfully to include this higher standard for arrest warrants.
The Greens also argue that the government has not properly justified why these new powers are needed and that their scope is "disproportionately large" compared to the threats they target.
Ms. Andrews said the changes will provide law enforcement agencies with the tools to keep up with technology.
She pointed to 290 arrests in Operation Ironside, which involved Australian and U.S. law enforcement cooperating to provide encrypted messaging services to criminal networks.
"This bill is just one more step the government is taking to ensure our agencies maintain that edge." She said.
"Under our reforms, the Australian Federal Police will have more tools to go after organized crime gangs, to keep drugs off our streets and out of our communities, and to those who commit the most heinous crimes against children."
The Human Rights Law Center blamed the government for pushing the bill through Parliament after it was debated and passed in the House of Commons on Tuesday before being passed in the Senate on Wednesday morning.
Kieran Pender, a senior lawyer at the center, said the law gives broad surveillance powers that will have a chilling effect on journalists and whistleblowers.
"Given that these powers are unprecedented and highly intrusive, they should have been narrowed to what is absolutely necessary and subject to strong safeguards," he said.
"It is appalling that instead of accepting [all] the committee's recommendations and allowing time to review the subsequent amendments, the Morrison government rushed these laws through in less than 24 hours."
The Law Commission of Australia said it was disappointed that it failed to adopt the judge's recommendation to issue an arrest warrant.
"These warrants have the potential to cause significant loss, damage or disruption to legitimate computer users who are not suspected of any wrongdoing," said Chairman Jacob Brasch.
He noted that the administration intends to consider these issues in other legislation, but said the committee's recommendations specifically address the "novel, extraordinary and intrusive" warrant-based powers in the legislation.
Security officials and law enforcement have been fighting for similar powers for years. Those powers were the subject of controversy after police raided the home of then-News Corp. reporter Annika Smethurst after she was leaked an earlier proposal for the law.