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The Prosecutor General's Office failed on a previous attempt to secure a warrant but will now be able to issue an application for the 87-year-old ethnic Latvian's extradition from Australia.
Kalejs was charged last month with crimes against humanity, genocide and war crimes, all relating to his role as commander of guards between June 1942 and July 1943 at Salaspils, a Nazi-run camp near Riga where thousands died.
Judge Vija Siliniece told the court she had taken into account the seriousness of the charges against Kalejs and his failure to answer questions put to him in Australia on behalf of Latvian investigators. She made no reference to documents produced by Juris Moculskis, Kalejs' lawyer, which showed, he said, that Kalejs is unfit to stand trial due to failing health. Together with his personality and considerable wealth, Kalejs' history suggests he may try to evade justice, said Liana Dadzite, representing the Prosecutor General's Office.
As evidence of Kalejs' wealth she pointed to the $750,000 he was able to pay in bail to U.S. authorities having been detained there in the late 1980s for failing to reveal his membership in the Arajs Kommando, a Nazi-sponsored Latvian death squad blamed for the deaths of about 30,000 Jews, Roma and communists.
His subsequent deportation from the United States in 1997 followed his deportation from Canada for the same reason in 1994. He hurriedly left the United Kingdom earlier this year after being traced to a retirement home in the English midlands.
Moculskis said he intends to file an appeal against the warrant.
Prosecutor's office spokeswoman Dzintra Subrovska earlier said any appeal attempt would not interfere with the extradition application process.
Welcoming the news of the warrant Efraim Zuroff, director of the Simon Wiesenthal Center in Jerusalem urged Latvia to act quickly in the already lengthy process.
"This progress is evidence of a growing willingness in Latvia to look at its past. The Latvian government must now take every measure possible as quickly as possible so that Kalejs will not escape justice," he said. "Every passing day is important. Latvia needs the trial and the education that will go with it."
Whether Kalejs might be jailed during extradition proceedings in Australia is unclear. Australian authorities are only saying that the initiative lies with the Latvian authorities to determine the next step.
But Melbourne Labor backbencher Michael Danby said Australian passport control could stop Kalejs from leaving the country pending the extradition request.
Zuroff rejected Moculskis' argument that Kalejs is suffering from cancer and dementia and is therefore unfit for a trial.
"Kalejs is among the healthiest war crimes suspects I've seen," he said.
He urged the Prosecutor General's Office to devote "the same energies" to the prosecution of 88-year-old Karlis Ozols, also of Latvian descent and resident in Australia. In addition to Ozols being a member of the Arajs Kommando, the Prosecutor General's Office has "irrefutable" evidence of his involvement in mass murders in Belarus, Zuroff says.
Speaking to The Age newspaper in Kalejs' home town of Melbourne, Eva Brenners, head of the local Latvian Society, expressed her opposition to a trial. More attention should be paid to pursuing the perpetrators of recent war crimes, such as Slobodan Milosevic, she said.