Von der Leyen was speaking to reporters on her first visit to Jordan where Germany has 280 members of its forces as part of the US-led coalition's battle against IS in Syria and Iraq.
The jihadist group "has been largely defeated militarily", the German minister said, adding however that the ultra-radical Islamist fighters "are not to be underestimated".
The battle must continue and IS must not be allowed "to retreat into safe havens", she said.
In October, Germany redeployed to Jordan military personnel and Tornado surveillance jets after withdrawing them from Turkey amid a dispute with Ankara.
Von der Leyen said Germany was now considering reducing the number of its troops in the region.
The IS self-proclaimed "caliphate" that spanned territory the size of Britain in Syria and Iraq was largely defeated last year.
Iraq announced the end of the three-year war against IS in December, and across the border in Syria the jihadists have been ousted from most of their strongholds, with only isolated pockets left.
Jordan, a key US ally, has used its own air force and allowed US-led coalition forces to use its bases to battle IS in Iraq and Syria.
The German defence minister also met Jordan's King Abdullah II and army chief of staff Mahmud Abdel Halim Freihat, and handed over two training aircraft and other military vehicles worth around 18 million euros.
"Germany and Europe... have a strong interest in Jordan's stability," she said.
The royal court said King Abdullah discussed with von der Leyen the "importance of intensifying cooperation and coordination among all concerned parties, regionally and internationally... to address the threat of terrorism".
Germany spent some 130 million euros on defence aid for Jordan last year. This included weapons, equipment and infrastructure, according to the German news agency DPA.
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