Immigration Minister Scott Morrison has suffered another defeat in the High Court after his attempt to grant a stateless refugee a temporary visa was ruled invalid.

The man, a Rohingya Muslim from Myanmar, arrived on Christmas Island in 2011 and tried to seek asylum in Australia. For two years the man, who was found to be a genuine refugee, was kept in detention as the Immigration Department assessed his eligibility for a permanent visa.

Court loss: Immigration Minister Scott Morrison. Credit:Alex Ellinghausen

But when Mr Morrison released the refugee early this year he only offered him a "temporary safe haven" visa, which has similar conditions as a temporary protection visa (TPV) and does not allow permanent residency in Australia. The decision, which was made by the minister without the man's consent, was ruled as "invalid" by the High Court on Thursday.

The blow comes as Mr Morrison has proposed offering TPVs for people who arrive by boat after July 19 and before December 31 last year, if the Senate allows the visa.