Contacts with the United States and South Korea "show that these countries were probably not aware of the presence of their two nationals on Burkina Faso territory", she added.
Two French soldiers were killed in the operation to rescue two French citizens who were kidnapped last week in neighboring Benin.
Officials said two French special forces officers and four "terrorists" were killed in Friday's pre-dawn military operation in northern Burkina Faso.
The two French soldiers who died were killed at close quarters as they entered one of the kidnappers' four shelters, the general said.
President Emmanuel Macron welcomed the hostages as they stepped off the French government jet on Saturday, less than 48 hours after French special forces stormed their captors' hideout in a daring night-time raid.
Al-Qaida and ISIS were known to operate in the area, officials said at the press conference, but they did not say that either of those groups, or any Islamist extremist groups, were involved.
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US officials were not immediately available for comment.
The hostages had been kidnapped in neighbouring Benin earlier this month.
It warns of "the presence of armed terrorist groups and the risk of kidnapping".
Their guide's body was found on Sunday, riddled with bullets, and the auto that he and the tourists used was found burned out across the border in Burkina Faso. In February, Burkina Faso said militants were increasingly active in West Africa and instability in the Sahel was spreading to coastal countries such as Benin and Ivory Coast.
Two French service members lost their lives during the nighttime raid to release the four from their 28-day ordeal. A military ceremony is planned for them next week.
Burkina Faso lies in the heart of the Sahel, a vast semi-arid region bordering the Sahara.
The country's military conducted exercises previous year amid concern about armed groups' activity in Burkina Faso, Niger and Nigeria.
The raid resulted in the death of two French soldiers.