Mr Juncker revealed the European Council is not united on matters of security and defence and called for a radical reform of the decision-making progress.
Speaking at the Munich Security Conference, Mr Juncker said the council could never reach the unanimity needed when it comes to taking important decisions affecting European security.
The EU chief seemed to take a swipe at German Chancellor Angela Merkel, claiming Germany is particularly reluctant to agree on decisions proposed by the EU Commission when it comes to defence.
He said: “We need to make our decision-making process much easier.
“We need to be able to work with a qualified majority in the European Union.
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“I said this in my speech on the occasion of the State of the Union in the European Parliament, and the commission also handed in proposals in that regards.
“When it comes to defence missions, we will never be able to make unanimous decisions on deploying soldiers, especially when it comes to Germany because Germany has a parliamentary army.”
Speaking at the conference before Mr Juncker, Prime Minister Theresa May called on EU leaders not let “rigid institutional restrictions” on working with a non-member state or “deep-seated ideology” undermine existing cooperation.
Mrs May proposed a new UK-EU security treaty that would underpin the relationship on security and data sharing.
She said there is “no existing security agreement that captures the full depth and breadth for a new relationship”, but added there are cases of agreements on areas like trade with non-EU countries.
She said: “There is no legal or operational reason why an agreement could not be reached on internal security.”
The Prime Minister has warned that refusing to do so from the Brussels would be a “political doctrine and ideology with real-world consequences for all our people in the UK and the EU”.