Abu Sayyaf was active in the Philippines years before linking up with Isis, and has supported its violent activities through kidnapping and demanding big ransoms.
Eight soldiers were also wounded, the military added.
The 59-year-old Dutch birdwatcher/photographer was killed when Filipino soldiers engaged in a 90-minute firefight with Abu Sayyaf militants on the island of Sulu, reports the Washington Post. He was kidnapped in the waters off Parangan village in Panglima Sagala, Tawi-Tawi on February 1, 2012 and was held captive by Sahiron's group in the hinterlands of Sulu.
"Military troops established blockade and encountered (Abu Sayyaf leader Radullan) Sahiron's group, composed of 30 fighters, at 7:41 a.m. today, leading to more than an hour of a gunfight that killed six bandits and wounded 12 more", Pabayo said.
Horn was on an expedition to photograph rare birds in Tawi-Tawi when he was abducted by unknown gunmen and turned over to the Abu Sayyaf.
The Dutch foreign ministry confirmed Horn died in an "exchange of fire", adding that it was investigating the exact circumstances of his death.
It earlier pledged allegiance to the al Qaeda militant group.
In December 2014, Vinciguerra fled his captors after overpowering one of the Abu Sayyaf men and killing him with a jungle knife.
"We express our deep condolences to Mr Horn's family and loved ones".
He said government forces "tried our very best to safely rescue him from his captors" and suffered casualties themselves. According to the statement, she was the wife of one of Abu Sayyaf's leaders.
Horn was 52 when he was kidnapped.
Patikul, a remote area of Jolo island that is part of the Sulu chain, is a known stronghold of the Abu Sayyaf, a small group of Islamic militants wanted for kidnappings, beheadings of hostages, bombings and acts of banditry in the south.
The military further stepped up offensives in late January this year after the cathedral twin bombings in Sulu's capital, Jolo, with the perpetrators linked to the group.
MAX jet grounded for at least 10-12 more weeks: IATA
This is perhaps the clearest admission so far from Boeing that at least one aspect of the aircraft's build wasn't done properly. We can't say for certain that an angle of attack disagree alert, which was missing, would have made a big difference.