A Somali asylum seeker taken by police to Auckland airport has won a temporary reprieve from deportation.

Immigration officials were stopped from putting Abdikarin Ali Haji on a plane out of New Zealand by a High Court challenge that was raced through at top speed as he was taken through the airport.

Haji was booked on a flight out of Auckland on Wednesday, but the court ordered he remain in the country until the government has read a report by the UNHCR on conditions in his native Mogadishu.

Haji made a desperate plea to onlookers as he was taken away by police.

"They are committing a crime on me man...they are committing a crime on me," he called.

Haji said the deportation was a violation of human rights.

He has been in New Zealand for more than five years, but all his attempts at asylum have failed. Now the government says it is time for him to go back, despite the risks in Somalia.

Associate immigration minister Damien O'Connor fronted up to media on Wednesday.

"There are many countries around the world that are dangerous, Somalia is one of those...that's been taken into account. But in the end we have a person who's illegally in this country and we have to deal with that."

Somalia has been embroiled in civil war for over a decade. Safety is an unfamiliar concept there and many Western countries, including the US, refuse to send anyone back.

Haji's lawyer Claudia Farry says she is relieved at the High Court's decision to stay the deportation.

The Somali was within two hours of being put on a plane to Africa when the judge's order keeping him in the country came through.

The immigration department has been told to consider a UN report on the situation

Meanwhile, Haji is back in prison.