Mr Weimar, best known for his time as Victoria's COVID-19 response commander, will lead a housing statement implementation group within the Department of Premier and Cabinet.
Department secretary Jeremi Moule signed off on Mr Weimar's appointment in consultation with Ms Allan, who backed the selection.
"He was absolutely appointed appropriately by the secretary of the Department for Premier and Cabinet," she told reporters on Monday.
Mr Weimar oversaw Victoria's COVID-19 Response unit from July 2020 to April 2022 and became a regular fixture of daily press conferences during the pandemic.
The former VicRoads and Public Transport Victoria chief executive then led the organising committee for the 2026 Commonwealth Games, before the government pulled the plug on the event in July.
In one of his final acts as premier, Daniel Andrews set a target to build 80,000 homes across Victoria each year over the next decade as part of the government's housing statement in September.
Jacinta Allan has labelled the opposition's claims as nonsense. (James Ross/AAP PHOTOS)
The Victorian opposition has raised concerns about the appointment process for the new deputy secretary role, questioning why it was not publicly advertised.
Opposition Leader John Pesutto zeroed in on whether Mr Weimar was told about the plum job before he appeared at the Commonwealth Games inquiry in October.
"We now see that he's been appointed to a $500,000 job without a merit selection process," he said.
"The perception of jobs for mates and cronyism is something that has to be investigated now given the timeline."
Ms Allan told reporters she could not recall if she and Mr Moule discussed other candidates for the job.
"Jacinta can't remember whether any other candidates were discussed in that phone conversation because, let's face it, there were no other candidates," Mr Pesutto claimed.
"Everybody knows that. This was Jacinta Allan looking after her mate."
When asked about the "jobs for mates" accusation, Ms Allan pointed to Mr Weimar's vast experience with complex and challenging areas.
"The Liberal Party might be running around out there with all sorts of conspiracy theories, all sorts of grassy knoll theories, it's nonsense," she said.
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