Diplomatic sources said earlier British objections to any suggestion the headquarters could have an operational military role had held up agreement but Federica Mogherini stressed the way was now clear, presstv.ir reported.
"I understand it is finalized. I understand we have a couple of days to have the official text in place," Mogherini told reporters after a meeting of EU defense ministers in Brussels on Thursday.
She stressed there was no holdup nor need to revisit the political decision all 28 member states took in March to set up the Military Planning and Conduct Capability (MPCC) facility.
There had been some expectations that after EU foreign ministers approved a text Monday, the formal launch could be announced Thursday.
A statement of conclusions agreed by the defense ministers said member states looked "forward to the effective establishment, as a short-term objective, of the Military Planning and Conduct Capability within the EU Military Staff in Brussels."
"The MPCC will assume responsibilities at the strategic level for the operational planning and conduct of the EU's non-executive military missions," it said.
The MPCC will initially coordinate three such missions, training government forces in Mali, the Central African Republic and Somalia.
Mogherini has led efforts for the EU to take on a much larger defense and security role given the uncertainties raised over Washington's commitment to European security by President Donald Trump.
Europe's worst refugee crisis since World War II and a series of deadly attacks linked to the Daesh terrorist group have also encouraged calls for the EU to do more.
Brexit-bound Britain has traditionally opposed any such moves toward a possible EU European army and prioritizes NATO over the bloc on defense.
Asked about Britain's future in EU security, Mogherini said all sides expected London to continue to play its full role until the Brexit divorce is completed.
"Obviously, once you are not a member state you cannot take part in the decisions but you can take part" in the missions, Mogherini said.