"We must show that ... we, Europeans, Germany and France in particular, are defending our common values and interests," Macron said at a news conference in the city of Toulouse.
Macron and Merkel, after holding bilateral talks and a joint French-German cabinet meeting, both said they were convinced the Brexit negotiations are in their final stages and that a deal can be adopted by EU leaders on Thursday.
Merkel stressed: "This is very intensive cooperation ... and the news we are hearing from Brussels could be worse, to put it another way."
Both leaders also attended a joint meeting on defense and security.
In a statement issued at the end of the meeting, both countries said they reached a legally binding agreement on the arms export rules regarding Franco-German military programs. They did not disclose details.
The agreement demonstrates "mutual trust" and allow both countries to work on developing key military equipment, including tanks and combat aircraft, the statement said. Macron's office said further steps were still needed before the deal can enter into force.
Both countries decided to halt weapons exports to Turkey after the offensive in northeast Syria last week. Germany has also banned defense industry exports to Saudi Arabia over the war in Yemen - while France has not.
Earlier Wednesday, Macron and Merkel visited the headquarters of plane-maker Airbus, widely seen as a symbol of European industrial cooperation, near Toulouse. The company, which is holding its 50th anniversary celebrations this year, has production and manufacturing facilities in countries including Germany, Spain and Britain.
The French and German delegations, including key ministers from both governments, also sought to improve cooperation on how to fight climate change and develop innovative technology. They said their "determination" to defend European new copyright rules against Google's decision last month not to apply them.
Macron also said France and Germany were working at organizing a summit with Ukraine and Russia "in coming weeks" to help resolve the conflict in Ukraine.
On Wednesday night, Macron and Merkel were having dinner with incoming European Commission President Ursula von der Leyen and members of the European Round Table of Industrialists, a group gathering over 50 major European multinational companies.
They were expected to discuss the U.S. decision to put tariffs worth $7.5 billion on EU goods like wine, cheese and olive oil, following a green light from the World Trade Organization in a case involving illegal EU subsidies for Airbus. The tariffs, to take effect Friday, will be 10% for EU aircraft and 25% for everything else.
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