Ban appealed "to all EU leaders to show leadership and compassion" when they meet on Wednesday, said his spokesman in a statement.
"The secretary-general is extremely concerned about the deteriorating situation facing refugees and migrants arriving across Europe," he added.
The United Nations has made repeated appeals to European leaders to uphold human rights as the continent grapples with its worst migration crisis since World War II.
Ban said he was worried about the closing of some borders in Europe, the lack of proper facilities to receive migrants and the increased detention of asylum seekers and migrants.
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Ban last week said he was "shocked" by the treatment of migrants in Hungary, where the government has sealed off the border with Serbia and police have used water cannons to push back refugees.
Hungary has also made border-crossing a crime punishable by up to five years in jail.
EU interior ministers will meet on Tuesday to try to coordinate their response to the crisis ahead of an emergency summit set to open on Wednesday.
Ban called on EU leaders to "forge a common approach which is in line with their international obligations and honours the letter and spirit of the United Nations charter."
Ban has called a meeting on September 30 on the sidelines of the UN General Assembly to ramp up the international response that the UN chief has said should be "humane, effective and rights-based.