By a vote of 86 to 50, Parliament said the former Conservative leader's actions have "eroded public confidence in Australian democracy" and made real accountability impossible.
It is the first time in Australian history that a former Prime Minister has been formally reprimanded by the House of Representatives.
For two years, Mr Morrison had self-appointed Minister of Finance, Home Affairs, Treasury, Minerals, Agriculture and the Environment, without saying so publicly and without inform the ministers in place.
"He owes the people of Australia an apology for undermining democracy," said Prime Minister Anthony Albanese, whose centre-left party ousted Mr Morrison in the May 2022 election.
The former head of government was present in the hemicycle for most of the debate and listened, impassive, to the denunciations of which he was the subject.
When he spoke it was to vigorously defend his actions and accuse the Labor government of partisanship, "political bullying" and trying to "impose its punishment".
Mr Morrison expressed some doubts about the confidentiality of his appointments and said he would have spoken about them to the public if asked by reporters.
"I acknowledge that the non-disclosure of the arrangements caused unintended offense and I apologize to those who were offended," he said.
But "I make no apologies for taking action, especially cautious layoff action, in a national crisis to save lives and livelihoods."
A recent inquiry, led by a former judge of the High Court of Australia, finds that these acts have been "harmful to confidence in the government" and recommends closing several legal loopholes allowing the appointments to remain secret.
Despite the outrage they may have caused, Mr. Morrison's actions were ultimately deemed legal.
The ex-Prime Minister has refused calls for the resignation of Parliament.
For his part, Mr. Albanese indicated that Parliament would try to change the law to ensure that ministerial appointments are made public.