Pope Francis concluded a successful five-day visit to the Philippines on Monday, but the security situation was not as placid as it seemed, say insiders within the authorities in charge of security.

Sources within the intelligence community, who were unnamed for reasons of security, told ABS-CBN News that the arm of Al Qaeda in the region, Jemaah Islamiyaah, was planning to carry out a bombing during the Pope's visit to the country.

ABS-CBN News reported that the intelligence community monitored reports of threats to the Pope, which included claims that the JI was planning an attack on the Popemobile using an improvised explosive device or IED.

A security official told ABS-CBN News that the threat was "very serious."

The Philippine government undertook a massive mobilisation of both the Armed Forces of the Philippines and the Philippine National Police as part of its security preparations for the visit of Pope Francis. The total number of police and soldiers deployed reportedly reached 40,000. These allegedly included armoured units and the Philippines' elite anti-terrorism unit, the Light Reaction Company.

The government also carried out additional security measures, including cutting off cellular network coverage in areas that the Pope passed by or visited, which included areas devastated by Supertyphoon Haiyan in 2013.

However, the Philippine government denied that they had to deal with a serious security issue during the Pope's stay in the country. Herminio Coloma Jr., secretary of the Philippine Presidential Communications Office, said that the mobilisations and measures were "part of the security preparations for the pope's visit."

Col. Restituto Padilla, spokesperson for the Armed Forces of the Philippines, also denied monitoring any direct threat to the Pope.

ABS-CBN News' sources in the intelligence and security side said that the Jemaah Islamiyah threat had confirmation from other intelligence outfits in the region.