The West African state has been divided into a rebel-held north and government-controlled south since a brief 2002-2003 civil war that began after an attempted coup.
An official at the army headquarters in the main city, Abidjan, said: "I confirm there were at least three killed in the attack this morning at the border with Ghana.
"Our forces are leading [search] operations in the area even if the situation is now under control."
The former French colony closed its land border with Ghana while investigations were carried out, officials said.
The attack occurred hours before foreign mediators met 150 km away in Abidjan to review progress on a foundering peace plan intended to reunite the world's top cocoa grower and pave the way for elections by the end of October.
Louis Michel, the EU's commissioner for development, who attended the meeting, said the country's foes had to throw their weight behind peace efforts to stop the decay in the once prosperous former French colony from spreading.
He said: "Progress is largely insufficient and the population's situation is deteriorating in the north and the south whether be it in terms of infrastructure, youth employment, teaching or social protection."
"It's urgent to unblock the current impasse," he said, calling for progress on a voter identification scheme which he said was vital to enable fair elections to take place.
He said that Charles Konan Banny, the prime minister, entrusted with implementing the UN-backed peace plan, did not have the necessary room for manoeuvre to do so and called on the country's foes to stop "blocking each other".
A police officer posted near where Friday's attack took place said two attackers had been arrested. He said the attacks were directed at the main border post with Ghana and a smaller checkpoint several kilometres inland.
In Ghana, Kofi Arthur, the western regional police commander, told Reuters the trouble had not spread over the border.
"Everything happened in Ivorian territory. It didn't spill into Ghanaian territory," he said.