The vandals, who police say acted sometime Saturday night or early Sunday morning, splashed paint throughout the cemetery and basilica and scrawled "Saint of Genocide" on a headstone.
Carmel police Sgt. Luke Powell said the incident was being investigated as a hate crime because the vandals targeted "specifically the headstones of people of European descent, and not Native American descent."
Serra, an 18th century friar who brought Catholicism to California, has been criticized by many for his harsh treatment of Native Americans. Despite protests, Pope Francis canonized Serra on Wednesday in a ceremony in Washington, D.C., saying the friar "sought to defend the dignity of the native community," and suggesting his legacy has been misinterpreted.
The Carmel Mission had planned an event Sunday celebrating Serra's sainthood. Instead, staff and volunteers spent the morning picking up statues and scrubbing off graffiti.
"Pray that the people [who] did this take responsibility for their actions on this sacred property and that they seek reconciliation," a mission representative wrote on Facebook. "Let us remember that we live in a loving community and let us not be discouraged by such things. As St. Serra said, "Always look forward, never back."
Powell said investigators were reviewing surveillance video to try to identify the vandal or vandals. There were several security guards stationed overnight at the mission, he said, but the vandalism went undetected until 7 a.m. Sunday.
Investigators were still pursuing leads, but had not received any tips from the public as of Monday morning.
"No one has claimed responsibility for the act," Powell said.
The Carmel Mission has seen an uptick in visitors in recent months in advance of Serra's canonization and as controversy has grown.
The Spanish missionary arrived in what would become California in 1769 and established nine missions between San Diego and San Francisco. He viewed the indigenous tribes as heathens who desperately needed the Gospel, and baptized thousands of Native Americans.
The Spanish brought diseases that devastated the indigenous population, and were known for flogging those who disobeyed and capturing those who tried to leave the missions. Serra's role in such violence is disputed, and the matter has been debated on university campuses and in the halls of the state Legislature.
This year, legislators attempted to replace a statue of Serra that sits in the National Statuary Hall Collection in Washington with a statue of
Those at the mission expressed shock.
"When I came out for Mass this morning, I was disappointed, but it could have been much worse," Carmel Mission Basilica pastor Father Paul Murphy told KSBW. "Being a saint doesn't mean a person is perfect. "We all have our flaws, we all have our defects, and so it was with Serra."
Anyone with details about the vandalism is urged to call police at (831) 624-6403.
Times staff writer Veronica Rocha contributed to this report.