The High Court has quashed Immigration Minister Scott Morrison’s efforts to prevent a stateless refugee from applying for permanent residency in Australia.

The asylum-seeker arrived on Christmas Island by boat in December 2011.

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Assessed as a genuine refugee after four months, the man was held in detention for more than two years while the immigration department determined whether he was eligible to apply for a permanent protection visa.

Once satisfied the man met the requirements, the department handed the decision over to Mr Morrison.

However, instead of making a ruling, Mr Morrison granted the man a temporary safe haven visa and a temporary humanitarian concern visa.

The granting of the safe-haven visa, which is only valid for seven days, then prevented the man from making a valid application for a permanent visa.

“It was not disputed that the minister granted the seven-day visa for the purpose of engaging the prohibition on making a valid application for any visa …” the court ruled on Thursday.

In a unanimous ruling, judges ruled the “grant of that visa was invalid” and quashed both visas.

Mr Morrison will now consider whether to allow the man to apply for a permanent visa.