The European Commission gave more than $7 million in aid to the WFP's operations in Somalia last year, a fraction of the donations of more than $1 billion it received, U.N. data shows.
EU member states gave much more money on a bilateral basis. It was not immediately clear whether any would also suspend aid.
Balazs Ujvari, a spokesman for the European Commission, neither confirmed nor denied specifically a temporary suspension but said: "So far, the EU has not been informed by its U.N. partners of a financial impact on EU-funded projects.
"Nevertheless, we will continue to monitor the situation and abide by our zero-tolerance approach to fraud, corruption or misconduct."