Pope Francis has warned against using religion to fuel conflict on his last day of his visit to Indonesia, the first stop in his tour around the Asia Pacific region.

At the Istiqlal mosque in the capital Jakarta, the Pope signed a declaration on religious harmony and environmental protection with the mosque's grand imam and met with local leaders of six religions.

The 87-year-old had earlier on Tuesday kicked off a 11-day visit to the region, the longest foreign trip of his papacy.

After celebrating mass before an anticipated crowd of 80,000 in Indonesia's main football stadium later in the day, he will move to Papua New Guinea, Timor Leste and Singapore.

Speaking at the mosque - the largest in South East Asia - the Pope on Thursday said people from different religions had to know "we are all brothers, all pilgrims, all on our way to God, beyond what differentiates us".

Humanity is facing a "serious crisis" brought about by war, conflict and the destruction of the environment, he added.

The Pope also visited a 28m (91ft) tunnel that connects Istiqlal mosque to a Catholic cathedral across the street.

He and grand imam Nasaruddin Umar stood at the entrace to the "tunnel of friendship", which he said was an "eloquent sign" of how people of different beliefs could share roots.

Indonesia is the world's largest Muslim majority country and only 3% of its 275 million are Catholics.

Indonesia has six officially recognised religions -- Islam, Protestantism, Catholicism, Buddhism, Hinduism, and Confucianism.

The Pope has ahead of him a gruelling schedule of public appreances and meetings with Church leaders in the Asia-Pacific, one of only a few places in the world where the Catholic Church is growing in terms of baptised faithful and religious vocations.

In Indonesia, he has been seen moving around and waving to adoring crowds from his wheelchair, underscoring concerns about his spate of health issues.

The Pope had earlier on Wednesday, the second day of his three-day visit, spoke alongside the country's outgoing president, Joko Widodo in Jakarta.

There, he said Indonesia should live up to its promise of "harmony in diversity".

He also praised Indonesians for having large families with up to five children.

"Keep it up, you're an example for everyone, for all the countries that maybe, and this might sound funny, (where) these families prefer to have a cat or a little dog instead of a child," he said.

His remarks were reminiscent of two years ago, where the Pope said having pets instead of kids diminishes the "humanity" of married couples.