After over two years, Berlin said it's still not ready to stop temporary passport controls at the Austrian border.
The ministry said in the memo, dated October 3: "Risk analysis... confirms the existence of a persistent level of threat". The Interior Ministry cited fears of a terrorist attack and unbridled migration for the prolonged checks.
The European Commission last month offered initial backing to a Franco-German proposal to allow more permanent border checks within the bloc's Schengen free-travel zone.
France, which imposed emergency border controls after Islamist attackers killed 130 people in Paris in November, 2015, is also keeping them in place for now.
It later came to light some of the attackers had entered the European Union by posing as migrants, and others had been able to travel undetected across several European Union borders in the lead up to the attack.
German Interior Minister Thomas de Maiziere said Berlin notified the European Commission, the EU Council, the European Parliament president and interior ministers of the EU-Schengen states about its decision.
Without waiting for the EC to implement reforms, applying the current regulations, these countries have already announced that they will extend the provisional border controls introduced in 2015 for another six months. "A complete return to a Schengen zone without border checks will only be possible once the overall situation allows it".
The EU Commission consequently ruled that the border controls could stay in place if there was a terrorist threat - a stipulation cited by Støjberg in her justification.