Macron's insistence on a freeze came as the EU's executive arm, the European Commission, recommended that the world's biggest trade bloc launch membership talks with Albania and Macedonia.
The Balkans spiraled into conflict in the 1990s as former Yugoslavia broke apart, but ethnic and nationalist tensions continue to simmer more than 20 years on.
The 28 EU member states must agree unanimously for any country to become a member. Accession to the bloc has been a powerful driver of political and democratic reform in countries like Albania, Bosnia and Herzegovina, Macedonia, Montenegro - which recently joined NATO - Serbia and its former territory of Kosovo.
But with Britain set to become the first country to leave the bloc next year, Macron told EU lawmakers in Strasbourg, France that "I will only support an enlargement when there is first a deepening and a reform of our Europe."
"I don't want a Balkans that turns toward Turkey or Russia, but I don't want a Europe that, functioning with difficulty at 28 and tomorrow as 27, would decide that we can continue to gallop off, to be tomorrow 30 or 32, with the same rules," he said.
But European Commission President Jean-Claude Juncker, whose institution recommends whether countries should be allowed in, insisted that Europe's door must remain open.
"If we remove from these countries, in this extremely complicated region, I should say tragically, a European perspective, we are going to live what we already went through in the 1990s," Juncker said. "I don't want a return to war in the Western Balkans."
When he took over at the European Commission four years ago, Juncker vowed that there would be no EU enlargement during his term.
EU and Balkans leaders will meet in Bulgaria on May 17, but no country in the region will be invited to join, even though some are involved in membership negotiations.
Announcing the European Commission's proposal for Albania and Macedonia to begin membership talks, EU foreign policy chief Federica Mogherini said the move "is an encouragement to these countries to continue on the path of reforms."
Macedonia's hopes have been on hold because of a dispute with Greece over the tiny Balkan country's name, although recent talks between both sides to end the stand-off have been progressing well.
Turkey is also a candidate for membership and has been promised fast-track accession negotiations in exchange for ensuring that tens of thousands of migrants - many of them Syrian refugees - don't enter Europe from its territory. However, the talks are at a virtual standstill.
Countries like France, Germany and Austria would prefer some kind of "privileged partnership" with Turkey to letting it join.
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