The warrant by a Munich court seeks the deportation or extradition of Demjanjuk, who lives in a Cleveland suburb and denies involvement in the deaths at Sobibor. His family says he is too sick to travel.
The U.S. Justice Department says Demjanjuk, 88, was a Nazi guard and can be deported for falsifying information on his entry and citizenship applications in the 1950s.
The U.S. Supreme Court chose last year not to consider Demjanjuk's appeal against deportation, clearing the way for his removal. But it had been unclear until Wednesday which country would take him -- his native Ukraine, Poland or Germany.
German Justice Ministry spokeswoman Eva Schmierer said it was not clear if the U.S. would automatically deport Demjanjuk, or whether Germany would have to formally seek his extradition.
The case that led to Wednesday's arrest warrant is based partly on recently obtained transport lists of Jewish prisoners who arrived by train at Sobibor during Demjanjuk's tenure at the camp from March to September 1943.
"In this capacity, he participated in the accessory to murder of at least 29,000 people of the Jewish faith," said the Munich prosecutor's office, which is handling the case because Demjanjuk spent time at a refugee camp in the area after the war.
His son, John Demjanjuk Jr., said in an e-mail to The Associated Press that his father is innocent, and is suffering from a blood disorder and acute kidney failure that makes him unfit for international travel.
"Whatever the Germans decide to do, we will continue to fight for justice in this sad case as there has never been any credible evidence of his personal involvement in even one murder, let alone thousands," Demjanjuk Jr. said. "He has never hurt anyone -- before, during or after the war. He is a good person as his family, grandchildren, friends and neighbors have always maintained."
Demjanjuk has said he served in the Soviet army and became a prisoner of war when he was captured by Germany in 1942.
He emigrated to the U.S. in 1952 and gained citizenship in 1958 but was extradited to Israel in 1986 after the U.S. Justice Department said it believed he was a sadistic Nazi guard at the Treblinka death camp known as Ivan the Terrible.
Demjanjuk spent seven years in custody before the Israeli high court received evidence that the Nazi guard was in fact another Ukrainian, and freed him.
Demjanjuk's U.S. citizenship was restored in 1998, but the U.S. Justice Department renewed its case, saying he had indeed been a Nazi guard and could be deported for falsifying information on his U.S. immigration paperwork.
A U.S. court ruled in December 2005 that he could be deported to Ukraine or to Germany or Poland. Demjanjuk spent several years challenging that ruling, until the Supreme Court decision last year.
"We hope that the process can be expedited to ensure that this Holocaust perpetrator will finally be appropriately punished," Efraim Zuroff, the top Nazi hunter at Israel's Simon Wiesenthal Center Zuroff told the AP by phone from Jerusalem. "We're on our way to a victory for justice today."
Munich prosecutors said Demjanjuk will be formally charged in front of a judge once he is extradited to Germany.