There is "something fundamentally wrong" in the way the home affairs department handles the repatriation of migrants, High Court in Pretoria Judge Eberhard Bertelsmann said on Friday.

"We have had the case of [Khalfan Khamis] Mohamed and the case of Emmanuel Tsebe, now we have the case of Edwin Samotse. Not only is it the same problem, but the failure to protect the fundamental right to life of an individual has raised its head again," said Bertelsmann.

"Again, the fundamental rights of an individual have been trampled underfoot. There comes a time where a court must [say] there is something fundamentally wrong in the manner in which the responsible department treats these cases."

The court was concerned at the way the department handled extraditions.

"The time has come to find out why this has happened again. The time has come to put it right. Surely a court must be concerned with the manner and fashion the department deals with issues of this nature.

"We know it has happened several times before. Courts have pronounced upon it but the results have been unsatisfactory," said Bertelsmann.

The court was reviewing a report by the home affairs and international relations departments on the unlawful deportation of Samotse, a Botswana citizen.

Samotse, a wanted murder-accused in his home country, was deported on August 13, 2014, despite a South African court order barring the extradition.

At the time, Samotse was in custody at the Polokwane police station while the Botswana government sought his extradition.

Crimes including murder, treason, an attempt to kill the head of state, and military offences of mutiny and desertion, are punishable by death in Botswana.

The court had found it was unlawful for the department to deport or surrender a foreign national facing the death penalty, if deported without the requisite assurance being obtained.

On Friday, Bertelsmann said there was "a hearsay allegation" indicating that Samotse had escaped jail in Botswana.

Maryna Steenkamp of Legal Aid SA and Steven Budlender of Lawyers for Human Rights, representing Samotse, said the report provided by the government departments was thin on detail.