Belgian Foreign Minister Hadja Lahbib
Brussels said the offices of Enabel, the Belgian development agency, had been destroyed in northern Gaza.
An official told AFP it took place on Wednesday.
It added that there were no employees in the building at the time of the bombing.
Belgian Foreign Minister Hadja Lahbib and Development Cooperation Minister Caroline Gennez spoke to Israeli Ambassador Idit Rosenzweig-Abu in Brussels.
"The ministers strongly condemned the bombing and destruction of the offices," the ministry said.
"The destruction of civilian infrastructure is absolutely unacceptable and does not comply with international law," it added.
Lahbib shared two images on social media on Thursday, one of an apartment building with a timestamp suggesting the photo had been taken on January 28, 2024.
The second image showed rubble from a destroyed building but there was no information about when it was taken.
The foreign ministry said the government had evacuated the agency's staff and immediate family members two weeks ago.
"We very much hope that these people -- including many children -- will be able to leave Gaza quickly and unharmed," it added.
Belgium has called for an immediate ceasefire to allow humanitarian aid into Gaza.
It will also raise the issue of compensation for the damaged infrastructure of projects financed by the European Union and member states with its EU partners.
The United Nations Conference on Trade and Development (UNCTAD) estimated that by late November, 37,379 buildings -- the equivalent of 18 percent of the Gaza Strip's total structures -- had been damaged or destroyed in Israel's military offensive.
Rami Alazzeh, a UNCTAD economist focused on assistance to the Palestinian people, said last month: "New data says that 50 percent of the structures in Gaza are (damaged or) destroyed."
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