The JI member, Dulmatin and another Indonesian, Mohammad Ali Abdul Rahiman, also known as Mauyha, were among those killed when aircraft targeted a meeting in the southern island of Mindanao on Thursday, said Colonel Gerry Jalandoni.
Jalandoni, who commands forces in the area, said intelligence operatives reported that two of three Indonesian JI members who were in the area of the airstrike were killed.
He said the military had found only seven ripped-up bodies in the marsh so far.
The military attacked after receiving information that the three JI members were meeting with leaders of the Abu Sayyaf Muslim kidnap group and with renegade members of the Muslim separatist Moro Islamic Liberation Front
Jalandoni said the military could not go deeper into the area to confirm the casualties because of the presence of the MILF which had signed a ceasefire with the government in 2002 to pave the way for peace talks.
The Abu Sayyaf are known mainly for kidnapping and bombing attacks against Christians and foreigners and have been linked by both Washington and Manila to the Al-Qaeda network of Osama bin Laden.
The Jemaah Islamiyah is considered the Southeast Asian chapter of Al-Qaeda and is blamed for the 2002 bombing in Bali, in which more than 200 people were killed.
The military has accused MILF commanders of sheltering JI members in Mindanao in violation of the ceasefire but the rebels deny this.