A Native American chief has blasted the pope's decision to canonize a controversial 18th century California missionary.

Pope Francis announced his decision to make Junipero Serra, a Spanish Franciscan friar who founded nine missions in the state, a saint on Thursday.

However he is now a controversial figure to due to his perceived mistreatment of the indiginous people, and it is believed he forced them to convert to Christianity despite resistance.

Anthony Morales, Chief Redblood of the Gabrielino Tongva Band of Mission Indians, said he was "stunned" and "angry" by the move, and is hoping the pontiff will reverse his decision.

"On all the 21 missions along the coast here our people were enslaved, they were beaten, they were tortured, our women were raped. It was forced labor and a forced religion," Morales said. "There's nothing saintly about the... atrocities on our culture, on our people."

Father Serra himself justified the beating of Native Americans, writing in 1780: "That spiritual fathers should punish their sons, the Indians, with blows appears to be as old as the conquest of the Americas; so general in fact that the saints do not seem to be any exception to the rule."

Father Edward Benioff of the LA Archdiocese defended the conduct of the controversial missionary.

"He lived in a very difficult time and he did the best he could under very difficult circumstances," Father Benioff said.

He also said elevating Father Serra to sainthood was a wise decision on the part of the pontiff.

"By canonizing a great missionary he's showing the whole church we're all called to be missionaries," Father Benioff said, "We're all called to share the love of Jesus with the whole world and to go out of our comfort zones and find those people who need hope."

Pope Francis has said he will canonize Father Serra in September, during a scheduled visit to the United States.

The pope's only official stop so far is a visit to Philadelphia for an international Catholic gathering, though he is also expected to attend New York to address the UN, and to visit Washington for a meeting with President Barack Obama.

"In September, God willing, I will canonize Junipero Serra in the United States, who was the evangelizer of the west of the United States," he told reporters on a plane taking him from Sri Lanka to Manila.

The pope said that because Father Serra has been considered a holy man for centuries, he had waived Church rules requiring a second miracle to be attributed to the candidate for sainthood after his beatification, adding that he was "a great evangelizer".

Father Serra was born in Majorca, Spain in 1713, and went to the Americas in the mid-18th century. He led one of the first Franciscan missions in California.

He arrived in San Diego in 1769, spending most of his life there before dying at a mission in Carmel near Monterey in 1784.