A total of 32 German soldiers based in Camp Taji near Baghdad were flown by a military transporter A400m to the al-Azraq airforce base in Jordan, the German military said in a statement.
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Three German soldiers stationed in Baghdad, the headquarters of the coalition fighting against the militant Islamic State group, were transferred to Kuwait.
"These troops can be brought back at any time if the training in Iraq is to resume," the statement added.
"The safety of our soldiers remains a top priority."
Germany has deployed about 415 soldiers as part of the anti-IS coalition, with about 120 of its troops stationed in Iraq.
Germany's move came after the Iraqi parliament passed a resolution asking the government to end its agreement with the US-led coalition.
Foreign Minister Heiko Maas said late Monday the basis for the Germany military presence in Iraq is "that we have an invitation from the Iraqi government and parliament."
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"If that is no longer the case... then the legal basis for us to be there is missing. We have to clarify this with those responsible in Baghdad as soon as possible."
Chancellor Angela Merkel, France's President Emmanuel Macron and British Prime Minister Boris Johnson had in a joint statement on Sunday urged Iraq to not jeopardise a battle against IS.
"Preserving the (anti-IS) coalition is of great importance in this context. We call on the Iraqi authorities to continue to provide the coalition with the necessary support," they said.
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