The 87-year-old is making only the third papal visit to the nation of 12 million people, the vast majority of whom are Christian.
Pope Francis disembarked from his plane and was received by a military guard of honour and a brass band that played the Vatican anthem.
He had flown from Indonesia, where he delivered a message of religious unity in the world's most populous Muslim-majority nation.
He appeared fit and smiling during his three-day visit despite a hectic schedule and intense heat, presiding over a mass on Thursday of more than 80,000 people at a football stadium in Jakarta.
Francis also signed a declaration in the Indonesian capital with the grand imam of Southeast Asia's largest mosque calling for action against religiously inspired violence and climate change.
He will stay until Monday in Papua New Guinea, the multi-ethnic Pacific country where the majority of the population is Christian, mostly Protestant.
The former Australian colony of 12 million inhabitants, visited by John Paul II in 1984 and 1995, is regularly plagued by tribal violence and saw deadly riots in January in the wake of anti-government protests against wage cuts.
Francis could also renew calls for greater protection of the environment in a country that has recorded extensive deforestation in recent decades and has been hit by natural disasters.
He is expected to focus on the spread of Christianity through evangelism on a one-day trip to Vanimo, a northwest Papua New Guinean town of 10,000 people.
On Monday he will travel to East Timor and then Singapore, where he will wrap up the longest and farthest tour of his 11-year papacy.
