The controversial President of the Philippines Rodrigo Duterte has written a personal letter to Pope Francis saying that the country values its "special relations" with the Holy See.

The letter comes after Duterte set himself on a collision course with the Catholic Church over plans to hand out millions of free condoms and reintroduce the death penalty.

However, the Pope is said to have told an aide to the President yesterday that he will bless Duterte after the aide handed the letter to Francis.

"When I had the opportunity of kissing the hand of the Pope, I said, 'Bless the Philippines, Your Holiness,' and his answer was, 'Yes, I will also bless your president," presidential adviser Jesus Dureza said in a video clip at St Peter's Square, shown on television on Thursday.

The Presidential Adviser on Peace Process Jesus Dureza released a photo of the President's letter to the Pope yesterday. It read: "Your Holiness, with profound respect, I have the honour to extend my own and my people's warmest greetings to Your Holiness."

Duterte's letter went on to recall the Pope's visit to the Philippines in January 2015. "Our countrymen remember Your Holiness' apostolic visit in 2015 with deep appreciation, knowing that it was made with the most sincere regard for the welfare of the Church's flock," he said.

"The Philippines values its special relations with the Holy See and regards with gratitude Your Holiness' gracious stewardship of the Catholic faith...Please accept, Your Holiness, the assurances of my highest esteem and respect."

The President had drawn criticism during the papal visit after calling the Pope a "son of a bitch" for supposedly causing a traffic jam during his visit. He later claimed his comment was aimed at incompetent officials.

Earlier this month, Duterte angered Catholics by ordering millions of condoms to be handed out in a bid to curb unwanted pregnancies.

The Church does not allow the use of condoms as a means of birth control and says abstinence and monogamy in heterosexual marriage is the best way to stop the spread of AIDS.

Separately, Catholic leaders and charities in the Philippines last month condemned as "very barbaric" Duterte's plan to restore the death penalty and execute "five or six" criminals each day despite what is widely acknowledged to be a corrupt legal system.

Duterte, 71, has made reviving the death penalty in the mainly Catholic nation his top legislative priority as part of a brutal war on crime that has killed 5,300 people.

"There was death penalty before but nothing happened. Return that to me and I would do it every day: five or six [criminals]. That's for real," he said.

An official at the Catholic Bishops' Conference of the Philippines said the Church "totally opposed" Duterte's plan. "The Philippines will be viewed as very barbaric," said Father Jerome Secillano, the executive secretary at its public affairs office. "It's going to make the Philippines the capital of death penalty in the world."

The Philippines abolished the death penalty in 2006 after strong opposition to capital punishment from the Catholic Church, to which 80 per cent of Filipinos belong.

Before taking office in June last year, Duterte vowed to introduce executions by hanging, saying he did not want to waste bullets and adding that he believed snapping the spinal cord was more humane than a firing squad.

Duterte said that he viewed the death penalty not as a means to deter crime but as retribution.