Universities were not consulted about changes to temporary foreign worker visas until after the overhaul was announced.
The decision to replace 457 visas and slash the list of 650 occupations which qualify by 200 was scrutinised by an advisory council including industries, unions and state governments, but universities were not represented.
"The universities had an opportunity then to respond to the announcements and we're working through a process with them to understand the nature of their concerns," immigration department deputy secretary Rachel Noble told a Senate hearing on Tuesday.
Universities have flagged concerns the changes will inhibit their access to the best and brightest minds from around the world including researchers, academics, and newly-graduated PhD scholars.
Labor senator Kim Carr was incredulous the research sector wasn't consulted sooner on the visa changes.
"Blind Freddy could have told you what their reaction would be," he said to immigration officials.
Immigration boss Michael Pezzullo said he relied on the employment, education and training departments to determine which jobs needed to be filled.
It was his team's job to go and fetch the talent from overseas.
"We're basically the HR department of Australia so we go out and recruit folks," he said.
"We're not the personnel strategy or workforce strategy, if you want to think of it in those terms, so we take advice from the relevant expert line department."
It was also up to the ministerial skills council to collate the list of occupations.
"We expect them to be across their brief and understand what Australia's skills needs are," Mr Pezzullo said.
He said government departments could consult on changes "to the nth degree" but people would always have issues.
"But you haven't consulted, that's the point. No degree here, none whatsoever," Senator Carr quipped back.
He then quizzed the immigration chief about how much correspondence he'd received following the visa crackdown.
"I wouldn't say we've been sort of overwhelmed but we have noticed the level of noise and the level of concern in some sectors and it can all be addressed," Mr Pezzullo said.
Ms Noble said it was not the government's intention to curtail research co-operation in Australia, and any unintended consequences could be rectified when the occupation list was revised every six months.
