MANILA (2ND UPDATE) -- Malacañang on Saturday said the nearly three-week crisis in Zamboanga City is now over.

Deputy presidential spokesperson Abigail Valte confirmed the statement of Defense Secretary Voltaire Gazmin that the conflict in Zamboanga is over.

"Certainly, the Defense Secretary made that announcement and we've always maintained in the days that we were dealing with the situation that it will be the officials on the ground who will be making the announcement based on their assessment," Valte said in an interview with state-run Radyo ng Bayan on Saturday morning.

"Our task from Day 1 is to ensure the safety of the hostages that were taken...as well as to get civilians out of harm's way and that has already been accomplished," she added.

The crisis began when members of the Moro National Liberation Front (MNLF) faction of Nur Misuari laid siege to the city last September 9.

Defense Secretary Voltaire Gazmin declares Zamboanga standoff over but still searching for Commander Habier Malik, the leader of the siege.

— Team AFP (@TeamAFP) September 28, 2013

The Armed Forces of the Philippines (AFP) on Friday said government troops had already rescued the last six civilians held hostage by the rebel group.

"We were told these were the last group of people held by the rebels. We now have accounted for 195 hostages," AFP public affairs office chief Lt. Col. Ramon Zagala said.

In an interview with ANC's "Dateline Philippines" on Saturday, AFP spokesperson Brig. Gen. Domingo Tutaan said security forces have already cleared majority of the areas where members of the MNLF faction of Misuari have been holed up since Day 1 of the standoff.

He said the military is now closing in on the remaining rebels who may still be hiding in the coastal areas of Barangays Sta. Catalina and Sta. Barbara.

Tutaan also said they are still searching for Misuari's top commander, Ustadz Habier Malik.

The AFP is now assessing the testimonies of the MNLF fighters who surrendered or were captured as well as the rescued hostages to locate the whereabouts of Malik, he said.

Gazmin: Mission accomplished

Meanwhile, a flag-raising ceremony was done at the Western Mindanao Command on Saturday. Gazmin, Interior and Local Government Mar Roxas and AFP chief of staff Gen. Emmanuel Bautista were present in the ceremony.

Gazmin said all hostages have already been accounted for and that their mission has been accomplished.

Roxas also confirmed that the 20-day siege in Zamboanga is finally over.

SILG Roxas, SND Gazmin w/ Mayor Climaco & local officials led flag raising ceremony & Tribute to soldiers pic.twitter.com/NZgni5WtNj

— zambocitygovt (@zambocitygovt) September 28, 2013

About 200 people, including 166 rebels, have been killed and more than 100,000 residents of the port city on the main southern island of Mindanao were displaced.

The AFP said 246 rebels have been captured, 7 of whom are females, 6 are minors, while the rest are males.

The fighting between government troops and the MNLF have resulted to the deaths of 12 civilians. Seventy-two more were injured.

The conflict has also left homes in ruin and brought businesses at a standstill.

An estimated P195 million was lost in fires that hit 9,523 buildings, houses, other structures in Zamboanga. -- With a report from Reuters