By Neil Jerome Morales

MANILA (Reuters) – One hundred days after militants loyal to Islamic State took over parts of a southern Philippine city, the military is confident the end is in sight for what has been its biggest security crisis in years.

After a lightning strike on May 23 on Marawi City, the Dawla Islamiya rebel alliance has held out against daily artillery bombardment and air strikes by jets and bombers, and its snipers remain placed in the rubble of the city’s business district.

But now, says Romeo Brawner, deputy commander of the military’s Marawi task force, rebel-held areas are shrinking, and there are signs the fighters are low on food and ammunition, and starting to flag.

“Hopefully, the Marawi siege is going to be over within the next few weeks,” he told reporters.

“Their strength continues to decline. We are inflicting casualties on them almost every day.”

The military has, however, missed repeated targets and deadlines to crush the rebels, whose strength and resolve it accepts it has under-estimated. The conflict in the southern region of Mindano has displaced hundreds of thousands of people and killed nearly 800 by government count – 133 soldiers and police, 45 civilians and an estimated 617 militants.

Residents say they fear the bodies of many more civilians could be in the rubble of the lakeside city. Estimates of civilians trapped in the fighting at one point were over 2,000, although authorities say 1,728 have been rescued.

The Red Cross says it is investigating the whereabouts of 179 missing people.

The protracted occupation has heightened concerns that Islamic State’s radical ideology may have gained a deeper foothold in the southern Philippines than was previously imagined, and raised questions about whether the military can contain a wider rebellion.

The presence of foreigners among the fighters is fanning fears that Mindanao could become a draw for extremists from Indonesia, Malaysia and Singapore, and those being pushed out of Syria and Iraq.

Armed forces chief Eduardo Ano said strategic gains had been made against the Islamist militants in the past week, including retaking the police headquarters and the city’s central mosque.

All routes in and out of Marawi had been sealed off, he said on Tuesday, and the hard core of about 50 rebels were preparing for their “last stand” and would have to decide whether to surrender, or be martyred.

NO WAY OUT

“That’s our main goal: No way out, no way in,” Ano said.

“If they want to go to heaven as they declared, we will give them the chance.”

The Marawi fighting has been the biggest security crisis of the presidency of Rodrigo Duterte, who declared martial law in Mindanao until the end of the year, and has urged lawmakers to approve funds to beef up the army by 20,000 troops.

On Wednesday, he said the conflict was by no means “the beginning and the end” of an extremism problem that stemmed from decades of separatist unrest.

Experts say the ability of two hardline groups from different parts of Mindanao – the relatively new Maute group, and the more established Abu Sayyaf – to carefully plan each step of the takeover of a city illustrates the ease in which extremists could organize and rally around Islamic State’s agenda.

The military says key to countering that will be whether it can kill or capture the main leaders, who it believes are still inside a conflict zone of about half a square kilometer (0.2 sq miles) in size.

One challenge will be securing what are believed to be dozens of hostages. Failure to do that could be a disaster for a military already criticized for the massive destruction caused by air strikes that have had mixed results. In two instances, the bombs have hit ground troops.

Duterte said the reason why the battle had gone on so long was because of the government’s desire to keep hostages safe and to avoid bombing a mosque where rebel leaders were believed to be taking shelter.

“It would have just created more animosity and outright hostility against the government,” he said.

Rodolfo Biazon, a former lawmaker and military chief, said that after Marawi is retaken, the government should seek more than a military solution and try to stop rebels from regrouping, by targeting recruitment and tackling radical ideology at the grassroots level.

“Remove the community support, and it will not last long. This should be the primary effort,” Biazon said.

“All Islamic radical groups should be targeted not physically alone, but psychologically by removing the water from the fish.”

(Writing by Martin Petty; Editing by Raju Gopalakrishnan)