Mr Morrison said the government had to keep an open mind on overhauling the migration program following this impact.
“We must re-look at the role that temporary visa holders play in meeting our economy’s workforce requirements, where Australians do not fill these jobs,” he said.
“Rather than taking Australian’s jobs, we need to instead appreciate how filling critical workforce shortages with temporary visa holders can actually create jobs elsewhere in the economy and, in particular, sustain growth and services in our regional economies.
"I can assure you this won't go away when the pandemic ends."
The latest federal budget has estimated a loss of 72,000 people from the migration intake for the 2020-21 financial year.
Net overseas migration is not expected return to positive levels until 2022-23.
The agriculture industry has been one of those hardest hit - with an estimated shortage of some 22,000 workers in horticulture alone, according to the Australian Bureau of Agricultural and Resource Economics.
Mr Morrison said the government could consider reviewing visa classes for sectors such as agriculture and hospitality - which have been reliant on temporary visa holders.
"What I'm saying is that we have got a very open mind on this," he said.
"This is a clear area where I think we are going to have to lean more forward on ... I see this as a value add.
"When Australians won’t do the jobs, the jobs still need to be done," Mr Morrison said.
Mr Morrison added this included possibly tailoring visa conditions to meet the workforce demands of regional areas.
“Conditionality is one of the great advantages of the temporary visa program. You can’t put conditions on permanent visas," he said.
“Those conditions can help us direct where people can go, which can ease pressures in metropolitan areas but hopefully ease pressures in regional areas.”
Labor’s immigration spokesperson Kristina Keneally said the government also needed to consider more permanent visa pathways in the migration system.
“We support migration – we see it as a tool that grows the economy,” she told SBS News.
“[But] we particularly are concerned about the high levels of temporary migration and we believe across a range of areas there should be greater pathways to permanency."