"We thank him for his service and call for an urgent cessation of violence in Sudan, and resumption of dialogue," he said.
Earlier, EU foreign policy chief Josep Borrell tweeted that the security of diplomatic premises and staff was a "primary responsibility" of the Sudanese authorities.
EU spokeswoman Nabila Massrali told AFP news agency the EU delegation had not been evacuated from Khartoum following the attack. Staff security was the priority and security measures were being assessed, she added.