The report on the ministries, handed down on Friday by former High Court judge Virginia Bell, labelled Mr Morrison's conduct as corrosive of trust in government.
Mr Morrison appointed himself minister of health, finance, industry, science, energy and resources, treasury and home affairs without the knowledge of most of the designated ministers.
The former prime minister said he welcomed the findings of the report and indicated he would not resign from parliament.
"At all times as prime minister I sought to exercise my responsibilities in a manner that would best advance and protect Australia's national interests and the welfare of the Australian people," Mr Morrison said in a statement.
"I note the criticisms made of my decision to be authorised to administer a series of departments where ministers had specific powers not subject to the oversight of cabinet.
"These decisions were taken during an extremely challenging period, where there was a need for considerable urgency. I note that the criticisms of my decisions have been made after the event."
The report found Mr Morrison had undermine public confidence in government, while it also reveals he sought advice on appointing himself to a sixth secret ministry.
Ms Bell says advice had been sought for Mr Morrison to appoint himself to the agriculture, water and environment portfolio in 2021, but the former prime minister did not proceed with the move.
She makes six recommendations in the report, including requiring public notifications of the appointment of ministers.
She also recommends publishing details of which ministers are appointed to administer departments and outlining different responsibilities when more than one is appointed to the same department.
The changes are set to be discussed when federal cabinet meets on Monday.
Prime Minister Anthony Albanese said the decisions surrounding the secret ministries were unprecedented and wrong.
"It is very clear that this is a scathing report which is an indictment on the Morrison government and the culture of secrecy," he said.
While Mr Albanese said his predecessor had misled parliament, he did not say whether Mr Morrison should resign.
Shadow treasurer Angus Taylor said the criticism over the secret ministries was a storm in a teacup.
"We'll work with the government on any reasonable proposals to provide clarity and transparency and that's absolutely fine," he told Sydney radio 2GB.
Independent MP Zoe Daniel, who supports the law change to prevent such things happening again, said she hoped Mr Morrison would "stand up in the parliament and unreservedly apologise to the Australian people" without having to be forced to do so by the privileges committee.
"Scott Morrison breached public trust in the extreme by appointing himself to secret ministries but by the time we found that out the public was already well onto the underlying problem and had thrown his government out of office due to concerns about lack of integrity."
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