A report by former High Court judge Virginia Bell into the multiple ministries found the secrecy surrounding the appointments he took on as prime minister was "apt to undermine public confidence in government".
"Once the appointments became known, the secrecy with which they had been surrounded was corrosive of trust in government," the report said.
"Given the parliament was not informed of any of the appointments, it was unable to hold Mr Morrison to account in his capacity as minister administering any of these five departments."
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.
While the former prime minister said he did so in relation to health and finance due to the pandemic, Ms Bell said this was unnecessary.
The report said while then-health minister Greg Hunt was told of Mr Morrison's moves, the federal health department was not.
It said Mr Morrison could have authorised himself to act as health or finance minister "in minutes", were the ministers to have been incapacitated due to COVID-19 in early 2020.
Ms Bell said Mr Morrison's other three ministries were in a "different category".
"These appointments had little, if any connection to the pandemic," she said.
"Rather, Mr Morrison was appointed to administer these departments to give himself the capacity to exercise particular statutory powers."
Prime Minister Anthony Albanese said the previous government had operated in a "cult of secrecy".
"(The secret ministries) were unprecedented and they were wrong. However members of the former government and current opposition enabled this culture of secrecy," he told reporters in Canberra on Friday.
"That is the characteristic of the Morison government. After nine years of chaos, a dysfunctional government has now been replaced by a dysfunctional opposition."
While he did not say whether Mr Morrison should resign from parliament, the prime minister said his predecessor had misled parliament.
The report also revealed the prime minister's office had instructed staff to prepare a brief for a possible appointment for Mr Morrison to be agriculture minister, which ultimately did not go ahead.
Ms Bell recommended six changes to be made including legislation requiring public notifications of the appointment of ministers.
She also recommended publishing details of which ministers were appointed to administer departments and outlining different responsibilities when more than one was appointed to the same department.
Mr Albanese said he would recommend cabinet implement all six recommendations to ensure "this breach of trust will never happen again".
The report confirmed Mr Morrison had only used his extra ministerial powers to veto the PEP11 resource exploration project off the NSW coast.
Ms Bell also took aim at Mr Morrison's decision not to tell ministers of his appointment to their portfolios.
"It is difficult to reconcile Mr Morrison's choice not to inform his ministers of the appointments out of his wish not to be thought to be second guessing them," the report said.
Mr Albanese said it showed a "lack of self-awareness" for Mr Morrison not to submit himself to an interview with Ms Bell for the inquiry but rather take part via his lawyers.
Ms Bell was asked by Mr Albanese to inquire into the portfolios issue after the solicitor-general found Mr Morrison's action had "fundamentally undermined" the principles of responsible government.
The solicitor-general found it was "impossible for the parliament to hold ministers to account for the administration of departments if it does not know which ministers are responsible for which departments".
The health and finance portfolio roles began in March 2020, while Mr Morrison started as industry minister in April 2021, and home affairs and treasury in May 2021.
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