Diplomats said the EU force would be backed by mechanized units and would operate under rules of engagement allowing it to defend itself and civilians.
The troops hope to secure Bunia and its airport and protect aid agencies and tens of thousands of refugees.
The 15-nation EU took over peacekeeping duties in Macedonia in March with about 400 troops, but received planning and logistical support from the NATO alliance, which includes the US.
The Congo mission is seen as a far bigger test of the union's effort to develop a military wing independent of NATO.
Last month, EU defense ministers declared that their rapid-reaction force -- a pool of 60,000 troops available at short notice for peacekeeping, humanitarian operations and regional crises -- was ready.
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