Pope Francis kisses a sick child before a canonization mass for Joseph Vaz in the Sri Lankan capital Colombo on Wednesday. The Pope is set to visit the Philippines on Thursday. Photo: AFP

 Philippine troops are facing a security "nightmare" during Pope Francis's visit starting Thursday, with potential stampedes, Islamic militants and lone-wolf assailants all ­concerns.

Nearly 40,000 soldiers and police are being deployed to protect the pontiff during his five-day trip to the Philippines, a majority Catholic nation where attempts have been made to kill visiting Popes twice before.

"This will be the greatest security nightmare that we can have," Philippine military chief General Gregorio Catapang said as he readied his troops for the pontiff's arrival.

Authorities have stated the huge crowds of devout ­Catholics are their main worry, with up to 6 million people expected for a mass in Manila on Sunday.

Huge crowds are also expected along his motorcade routes in the capital, while a one-day trip to typhoon-­devastated communities in the central Philippines will pose its own problems.

In a nationally televised address on Monday, President Benigno Aquino pleaded with his countrymen planning to join the crowds to remain calm and avoid creating a stampede that could endanger the Pope.

"I ask you, do you want ­history to record that a tragedy involving the Pope happened in the Philippines," Aquino said.

Aside from a crowd ­potentially crushing the Pope, Aquino also warned that ­blocking his motorcade would make him an easy target for an assailant.

The president referred to the threat of "terrorism" and an assassination attempt on John Paul II at the Vatican in 1981, as he called on all Filipinos to help protect Pope Francis in the ­Philippines.

Adding to the concerns, the 78-year-old pontiff has insisted he will not travel in a bullet-proof "popemobile" so can he be closer to his flock.

Highlighting the priority Aquino has placed on security, he personally led a late-night dry run on Tuesday of the ­motorcade journey that the Pope will make from the airport after he arrives - with ­thousands of police lining the roads.

A million worshippers packed the Colombo seafront to greet Pope Francis as he canonized Sri Lanka's first saint on Wednesday in the biggest public celebration the city has ever witnessed.

Many had waited through the night to see the first pope to visit the island in two decades canonize Joseph Vaz, a 17th century missionary who disguised himself as a beggar to evade persecution.