Defense Minister Herve Morin acknowledged that it could have been a French bullet that killed hostage Florent Lemacon, during an operation that demonstrated the risks of using military force against sea bandits.
Pirates seized a sailboat carrying Lemacon, his wife, 3-year-old son and two friends off the Somali coast a week ago. On Friday,.
Two pirates were killed, and Lemacon died in an exchange of fire as he tried to duck down the hatch.
"There will be of course a judicial inquiry, therefore there will be an autopsy. We cannot of course exclude that during the exchange of fire between the pirates and our commandos, the shot (that killed Lemacon) was French," Morin said on Europe-1 radio.
Still, he defended the action.
"We, I believe, made the best decision possible," he said.
France has been at the forefront of multinational anti-piracy efforts to protect the strategic shipping zone in the northern Indian Ocean - and has been more aggressive than many governments in responding to the seizure of boats holding its citizens.
The president of Somalia's northeastern region of Puntland, the main hub for the country's pirates, called on other nations to follow France's example.
"We call on any country whose citizens are taken by pirates to use force, because paying a ransom would only encourage more piracy," said Abdirahman Farole.
France's government has in the past said it refuses to pay ransoms. In this case, exceptionally, Morin said French negotiators discussed a ransom with the pirates, but they refused it.
Friday's operation was the third such raid by French commandos against pirates in the past year, but the first to result in the death of a hostage.
The pirates fired with Kalashnikovs as eight commandos boarded the boat backed by firepower from 70 commandos on three French frigates.
Three pirates were taken prisoner in the operation, and are to be brought to France for criminal proceedings, joining 12 pirates already jailed and awaiting trial here.
The four freed hostages were brought to Djibouti, and were to be flown to a French military airbase on Sunday, Morin's office said. Lemacon's body was to be brought to France later for an autopsy.
President Nicolas Sarkozy ordered the assault when all negotiations failed and the boat drifted toward the Somali coast, Morin said. France's policy is to refuse to allow French citizens to be taken ashore as hostages.
The French rescue operation did not appear to be anywhere near the standoff between an American cargo ship captain and his Somali captors. Pirates threatened to kill the U.S. captain after he jumped in the water Friday in a desperate attempt to escape.
Both countries are part of anti-piracy task forces and patrol the risky waters around the Gulf of Aden and other parts of the Somali coast.
There have been 65 pirate attacks in the region this year, and 15 vessels are currently held by pirates, with 243 hostages in the hands of pirates, according to the French Defense Ministry.
By Associated Press Writer Pierre-Yves Roger; AP writer Mohamed Olad Hassan in Mogadishu, Somalia contributed to this report