Aquino flew on Wednesday to Jolo island, where the Abu Sayyaf group is based and believed to be holding Norwegian resort manager Kjartan Sekkingstad, to meet with troops tasked with tracking the militants through hostile jungle terrain.
"We are getting a clearer picture of what is happening here. We saw today how to refine our operations so we can successfully rescue the remaining hostages," Aquino told reporters travelling with him.
Aquino also said he apologised to Canadian Prime Minister Justin Trudeau for the murders of the two Canadian men, who were abducted along with Sekkingstad and Filipina Marites Flor from aboard yachts at an exclusive southern marina nine months ago.
Retiree Robert Hall was beheaded on Monday after the Abu Sayyaf's demands for a ransom of 300 million pesos ($6.5 million) were not met. His friend, John Ridsdel, was beheaded in April after a similar ransom demand was not paid.
The Abu Sayyaf is a loose network of a few hundred Islamic militants formed in the 1990s with seed money from Osama bin Laden's Al-Qaeda network that has earned millions of dollars from kidnappings-for-ransom.
It is a radical offshoot of a decades-long Muslim separatist insurgency in the south of the mainly Catholic Philippines that has claimed more than 100,000 lives. The main Muslim rebel groups do not generally engage in kidnappings-for-ransom.
The Abu Sayyaf's strongholds are Jolo and nearby Basilan, small but mountainous islands roughly 1,000 kilometres (600 miles) from Manila with mainly Muslim populations.
Aquino, who is due to step down on June 30th, said he had found it difficult to end the Abu Sayyaf threat during his six years in office.
Among the problems, he cited the Abu Sayyaf's support of the local Muslim communities, many of whom have received money from the militants, he said.
"They [the militants] have many resources. They can buy sympathy and we are in their place of origin. They have knowledge of the terrain. All of the advantages are theirs," Aquino said.
He also said the military and police were understaffed, not having increased in size since 1986 despite the huge rise in population since.
The Abu Sayyaf is believed to be holding at least eight hostages, according to Pacific Strategies and Assessments, a regional security analysis firm.
These include a Japanese treasure hunter kidnapped in 2010 and a Dutch bird watcher abducted in 2012.