Down Syndrome Association Victoria executive officer Catherine McAlpine said the decision failed to acknowledge the positive contribution of a person with down syndrome.

"This unfair process is discriminatory and fails to acknowledge the contribution a person with down syndrome can make to society," she said.

"It also fails to acknowledge the contribution their family can make, as is the case here.

"It is unfortunate that applications for permanent residency by a person with down syndrome are usually rejected as the person is automatically judged as likely to incur significant cost to the Australian community.

Awakenings Festival director Jacinda O'Sullivan said the decision was discrimination against people with disabilities.

"Given all the proactive disability work that is being done in state and federal government, this is totally contradictory to all of that," she said. "It's contrary to the work being done to ensure human rights of all people with disabilities."

Wimmera Development Association regional skilled migration project manager Janet Heard said she was disappointed and saddened by the news.

"From a community perspective, Dr Moeller is a person with a child with a disability that requires support," she said.

"He is also a person in his community who is really needed. We have regional skills shortages and his position is so important to us.

"As a project manager for the Global Skills for Provincial Victoria program, which is centered around encouraging skilled migrants to apply for permanent residency, this situation seems at odds with the program's concept."