An immigration lawyer is planning a High Court challenge to the Federal Government's decision to cancel thousands of skilled migration applications.

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Visa applications for about 16,000 people and their families will not be considered, because the Government last month set a new cap on some skilled migration categories.

The move affects people living in Australia and around the world who applied several years ago for so-called offshore visas under three visa types - 175, 176 and 475.

The Federal Government says all those places are now full and the scheme is closed.

Some applicants have contacted the ABC describing the decision as "shocking" and "unconscionable".

The so-called 'cap and cease' decision was made by former assistant minister for immigration Michaelia Cash before she left the portfolio late last month.

Immigration lawyer Christopher Levingston, the treasurer of the Migration Alliance, has started proceedings in the High Court to challenge that decision.

"We're proceeding on the basis that the minister just didn't have the authority or the power to cease and cap these cases," Mr Levingston said.

He said there was some precedence in the court for such a challenge.

"(Senator Cash) was an assistant minister, and there is a case in the High Court decided some years ago that turns upon the appointment of the assistant minister."

A statement given by the Department of Immigration and Border Protection said the skilled migrants affected were in a "low priority" category and would have had trouble finding jobs in Australia.

"Most of the offshore applications in Priority Group 5 were for occupations that are not currently in demand on the Skilled Occupation List," the statement said.

"This means that they would be less likely to get a job if they migrated to Australia permanently."

Mr Levingston said the applications should have been given due consideration.

"It wastes this resource of all these people who were highly qualified, these people have been waiting in some cases up to eight years while these applications have been languishing."

Bangladeshi man Amos Deori has been living in Rockdale in Sydney's south for six years, and has been affected by the decision.

He applied for a skilled migration visa back in 2009, and has been waiting since then to find out if he, and his wife and son, will be approved for permanent residency.

Mr Deori was recently told that the Immigration Department had cancelled his family's application.

"I came to know a couple of weeks ago my application will be not processed further, and after this situation I'm disappointed, I have no hope now," Mr Deori said.

Since he applied for a skilled migration visa back in 2009, Mr Deori stayed in Australia on student visas, trying to study to meet the necessary requirements to get his application approved.

He estimates he has spent about $100,000 and is now worried it was a waste of money.

"I lost many things, I lost especially my hope for the future, to stay in Australia."