About 170,000 migrants have entered Slovenia since mid-October, when Hungary closed its border with Croatia. Many are heading to northern European countries such as Germany.
Slovenia's Prime Minister Miro Cerar said the fence was not aimed at closing the border, but at better controlling the flow of people.
On Wednesday, 14 people, seven of them children, drowned when their boat sank off Turkey, the country's state-run Anadolu news agency reported.
Europe is currently undergoing its worst refugee crisis since the end of World War II, in a large part driven by the four-year civil war in Syria. Other migrants have entered the continent from countries including Sudan, Somalia and Eritrea.
More than 60 African and European leaders gathered in Malta on Wednesday for a summit that European Council President Donald Tusk said "is about action, concrete and operational action."
Announcing a $1.9 billion emergency fund to offer people in Africa "a better future," Tusk said that EU governments are between them reviewing an all-time record of more than a million asylum applications.
"With our African partners, we have a shared challenge which is much more profound than a refugee crisis," he said in a statement Tuesday. "It is long-term, structural, deeply rooted in the economic situation of Africa where even economic growth does not entail immediate job creation but rather triggers social inequalities and increased urbanization."
Tusk said African nations can work with the EU to make more progress on reducing poverty, preventing conflict, and taking back migrants who don't qualify for visas and aren't refugees by the end of 2016.
"We will help African governments to re-integrate their own nationals and offer them meaningful socio-economic opportunities, including by funding training and educational programmes," he added.
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