Juncker reprimanded EU member states at a summit in Brussels for having pledged only 200 million euros of the 1.8 billion euros (USD 2 billion) they are expected to contribute to the trust fund launched in 2015.
"Member states are not delivering at a sufficient degree when it comes to pledges and commitments to the African Trust Fund," Juncker told a press conference ending the summit of 28 leaders.
"This is not acceptable and I urge colleagues to do more," Juncker said.
Member states are supposed to match that amount, but since then they have only pledged 200 million euros and disbursed just 89 million euros, according to commission figures.
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The Commission increased its share to 2.6 billion euros in the interim to make up part of the shortfall.
The fund is meant to help finance development projects and so ease the poverty driving migrants to Europe, which faces the biggest migration crisis since World War II.
The two-year plan is to relocate 160,000 Syrians and others fleeing war and persecution by September. Until now, only around 20,000 have been relocated to other member states.
The European Commission, executive of the 28-nation EU, earlier this month launched legal action against Hungary and Poland for refusing to take any asylum seekers and against the Czech Republic for effectively dropping out of the plan.
The move starts a long process that could result in fines.