Neither Misuari nor the suspect, identified as Assa Asmawil, was around when the raiders arrived, but a search of the compound yielded three boxes of bullets and grenades.
Misuari was reportedly in Jolo, Sulu during the raid, but his wife, Tarhata Ibrahim, was at home.
Chief Inspector Jose Ba-yani Gucela clarified that the raid was not aimed at Misuari. Gucela added that the raiders did not enter the home of the MNLF chieftain, who signed a peace agreement with the government in 1996.
Misuari, governor of the Autonomous Region in Muslim Mindanao, is also a government envoy to Muslim countries.
Misuari aide Jamasali Abdurahman branded the raid as a "blatant violation of the peace agreement" and a "slap on the face of the MNLF."
Abdurahman said he did not know Asmawil and denied the ammunition was for the Abu Sayyaf, which he called an "enemy of the MNLF."
The police did not specify the connection between Asmawil and Misuari, but residents said only people close to the MNLF leader were allowed to live in the compound.
Presidential Spokesman Rigoberto Tiglao said Misuari and his wife apparently were not aware that their place was being used for gunrunning.
"It could not be pinpointed to whom the guns are sold, but police suspected these could eventually end up in the hands of the Abu Sayyaf," Tiglao said.
He said President Arroyo has instructed Presidential Adviser on the Peace Process Eduardo Ermita to talk to Misuari and explain the raid.
Lt. Col. Danilo Servando, spokesman for the AFP’s Southern Command based in Zamboanga City, said an investigation will be launched to determine if the ammunition came from the military as indicated by the box that had the markings "DND" (Department of National Defense).
Servando also said they were not ruling out the possibility of pilferage.
Under the 1996 peace accord, the MNLF was under no obligation to disarm at once, and still maintained military-style camps in Mindanao, although about 1,000 of its fighters have been integrated into the Armed Forces.
Troops running after a large band of Abu Sayyaf bandits holding at least 21 American and Filipino hostages in Basilan have clashed in recent weeks with armed groups believed to be MNLF members protecting the Abu Sayyaf terrorists.
The military said the Abu Sayyaf gunmen fled into MNLF territories to evade the troops.
The Abu Sayyaf claimed they were fighting for an independent Islamic state in Mindanao, but engaged in mass abductions for ransom, victimizing mostly foreigners.
On May 27, they swooped down on the upscale Dos Palmas resort off Palawan and rounded up 17 guests, among then three Americans, and three workers of the facility.
The victims were taken by boat across the Sulu Sea to Basilan island in the South where the bandits also seized four hospital staff members and 15 workers of a plantation.
Thirteen of the Dos Palmas captives have been freed amid rumors of multimillion-peso ransom payments, while two others have been executed, one of them by beheading.
Abu Sayyaf leader Abu Sabaya also claimed they have chopped off the head of 40-year-old Guillermo Sobero of Corona, California, although his body has not been found.
The bandits likewise decapitated two of the plantation workers.
Some 5,000 soldiers have been deployed to Basilan to carry out a continuing offensive primarily meant to rescue the hostages.
Army Maj. Alberto Gepilano, spokesman for Task Force Comet undertaking the all-out offensive in Basilan, identified the captured rebel as Isset Imam Yusop, alias Issaf Abbas and Ibnurasid Balahim Ayud.
The troops also confiscated a pumpboat believed used by the rebels in transporting their members to neighboring islands.
In another development, a rebel-integree in the military was reported wounded in a clash with suspected Abu Sayyaf gunmen in Siasi town in Sulu.
Servando said the troops were on patrol when they encountered the bandits led by Commander Andil in North Laud at about 6 p.m.
Casualties on the enemy side could not be immediately determined.
Meanwhile, government prosecutors tasked to handle the kidnapping-for-ransom cases against suspected Abu Sayyaf members and supporters may yet get extra pay, insurance coverage and a gun for personal protection.
Justice Secretary Hernando Perez directed Chief State Prosecutor Jovencito Zuño to study the possibility of granting hazard pay and other benefits for performing their task in a so-called "war zone."
Among the 12 prosecutors dispatched to the South were Richard Anthony Fadullon and Perfecto Lawrence Chua Cheng.
Also yesterday, security at the justice department was tightened following a call from the Intelligence Service of the Armed Forces of the Philippines that there was a threat against Perez.
In Congress, Pangasinan Rep. Jose de Venecia Jr. said he will create a special Lakas committee that will draft an action plan that would encourage the surrender of Abu Sayyaf rebels and implement an anti-poverty program in Sulu and Basilan.
De Vencia said the plan was envisioned to be the ultimate solution to the Abu Sayyaf menace. — With reports from Marichu Villanueva, Delon Porcalla, Christina Mendez, Nestor Etolle