The operation began as part of a Belgian judicial probe of Amaq, the media agency of the banned jihadist group, and involved international officers from Europol.
Federal prosecution spokesman Eric van der Sypt confirmed the operation to AFP but he could not give a detailed breakdown of sites and accounts targeted.
"We've knocked them down for the moment," he said. "But we're not naive. A first cyberattack in 2018 didn't stop them from bouncing back."
Officers plan to reveal more about the operation at a news conference later in the day at Europol's HQ in the neighbouring Netherlands, he said.
Belgian agents were involved in a wave of cyberattacks against Amaq last year, but the spokesman admitted they had been surprised by how quick the sources returned.
In March 2016 the Belgian capital Brussels was hit in a double suicide attack claimed by the Islamic State that left 32 people dead.
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