Filipino police and soldiers threw up a massive operation involving nearly 40,000 personnel to protect the pope during the January 15-19 visit, which went off without any reported security incidents.
"Around the time of the papal visit, there was unsubstantiated intelligence about a Malaysian national who supposedly had a plan, either through a backpack or a vest, to be a suicide bomber," Roxas told reporters.
"But we followed all the leads and we found no substantiation," he said without elaborating.
Authorities had previously said his visit was a "security nightmare".
He shunned the armoured "popemobiles" used by his predecessors, preferring to use an open vehicle that allowed him to reach out and touch the masses that thronged to see him.
Despite the challenges, including an open-air mass in Manila that drew a record six million people on January 18, the visit went off without any serious incident.
The Philippines, which has suffered bomb attacks blamed on armed groups from the country's Muslim minority, has now been visited four times by three popes.
And one week before John Paul II's second visit in 1995, police uncovered a plot by foreign Islamist extremists to kill him by bombing his Manila motorcade route.
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