Foreign Minister Bernard Kouchner contacted the Sudanese government on Monday night.
"We are worried because two men were targeted with a burst of fire from about 10 meters (yards) away," Morin said. "They found themselves about 10 meters from forces that a priori were Sudanese. They immediately gave their identity and were engaged."
The two soldiers, special forces troops doing reconnaissance, were "unfortunately" not able to fire back, Morin said. The two were one-two miles inside Sudan, he said. The border is not marked, he added.
Later, French troops went to the area to try to find the missing soldier; they were fired on and fired back, said Morin.
Morin said France has asked Sudanese authorities for help in locating the missing soldier.
Sudan has been hostile to the European mission that was to involve at least 14 countries and 3,700 troops.
The mission, known as EUFOR and being deployed in Chad and the Central African Republic, is aimed at protecting refugees from the neighboring Sudanese region of Darfur and people displaced by fighting in Chad and the Central African Republic, some of it linked to unrest in Darfur.
The mission has been delayed by logistical problems and recent fighting in Chad.
Morin suggested that the Sudanese troops acted more out of instinct than politics.
"I think we find ourselves in a situation where soldiers whom we believe to have been Sudanese found themselves facing two men, two soldiers, and very likely out of reflex decided to use their weapons," said the French minister.
Sudanese media reported Tuesday that France's ambassador to Khartoum was summoned by the government for an explanation and that Sudanese border guards were involved.
"One Sudanese soldier was reportedly killed and some civilians injured," Sudan's pro-government Al-Sudani newspaper reported Tuesday.
There are currently 700 EUFOR troops on the ground, mostly French, Irish and Swedes.
Ireland, which has committed about 400 troops to the force, said it was undeterred by Monday's incident.
"The urgent necessity to provide security and assistance to 400,000 refugees and displaced persons affected by the situation in Darfur remains," Ireland's defense department said in a statement Tuesday.
In a separate statement Tuesday, the force's overall commander, Irish Lt. Gen. Pat Nash, appealed to the Sudanese authorities for any information on the whereabouts of the missing soldier. Nash expressed regret over the incident but also insisted it would not affect the force's overall mission.
About 70 Austrian troops left for Chad Tuesday to join about 75 Austrian soldiers already there, Austria's Defense Ministry said Tuesday.
A total of roughly 160 Austrian peacekeepers were expected to be in Chad by the end of March. Austrian Defense Ministry spokesman Maj. Wolfgang Schneider said authorities were aware of Tuesday's incident but that, for now, Austria planned to stick to its deployment and work plan.