"There is no account where debts are registered with NATO," Von der Leyen, a close ally of Chancellor Angela Merkel, said in a statement.
She also noted that NATO spending should not be the only criteria used to measure Germany's military efforts.
Yesterday Trump had tweeted that "Germany owes vast sums of money to NATO & the United States must be paid more for the powerful, and very expensive, defense it provides to Germany!"
His tweetstorm came a day after Trump met Merkel in Washington, where the two leaders showed little common ground over a host of thorny issues, including NATO and defence spending.
Merkel said Berlin had committed to increasing its military spending to two per cent of GDP, a target NATO member states formally agreed in 2014 to reach within 10 years.
Germany, whose wartime past has led it traditionally to be reticent on defence matters, currently spends 1.2 per cent of GDP.
Von der Leyen said today that Germany's increased military spending would not only go to NATO but would also be used for participating in UN and European peacekeeping missions and to contribute to the fight against the Islamic State extremists.
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