US President Barack Obama has led an impassioned funeral service for a popular black minister and politician killed in a church massacre, concluding with a rendition song of Amazing Grace.

Touching on the themes of racism, poverty and injustice that persist for African Americans in the United States, Obama said the killing of Reverend Clementa Pinckney – a personal friend – and eight others in a church was a call to grace.

The alleged killer did not know he was “being used by God”, he said on Friday.

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“Blinded by hatred, the alleged killer could not see the grace surrounding Reverend Pinckney and that Bible study group,” Obama told thousands gathered in the arena of the College of Charleston.

“The alleged killer could have never anticipated the way the families of the fallen would respond when they saw him in court in the midst of unspeakable grief, with words of forgiveness,” Obama said.

Behind him stood dozens of purple-and-black-robed ministers of the African Methodist Episcopal church.

The song Amazing Grace was the theme of his 40-minute eulogy, which the president ended by singing the traditional hymn, leading thousands of voices through the verse.

He called on his listeners to “prove” themselves worthy of this grace by waking up “to the way past injustices continue to shape the present”, by considering what “causes so many of our children to hate”.

And he said “God’s grace” would be expressed by doing something about the fact that 30 people are cut down every day by gun violence.

Pinckney and the eight other black worshippers were slaughtered last week at the historic Emanuel African Methodist Episcopal Church in Charleston, South Carolina.

Their alleged white killer had joined the prayer and Bible service for an entire hour before standing up and shooting them.

Pinckney’s funeral service is the third of the nine funerals to follow the killings. Thousands started lining up early in the morning for the service.

Pinckney, 41, was a senator in the South Carolina legislature and had been one of the earliest supporters of Obama’s presidential bid. The two met in 2007 as Obama was getting his campaign off the ground.

His ancestors had been preachers and civil rights activists, and Pinckney followed in their footsteps, “in the pulpit by 13, pastor by 18, public servant by 23”, Obama noted.

The killings shocked the nation, coming on the heels of a year-long series of killings of unarmed black suspects by white police officers.

But while those killings fractured communities and spawned violent riots, the killings of the nine in Charleston not only pulled people together in Charleston, they also provoked a deep soul-searching across the old South.

Black politicians, rights activists and conservative Republicans pointed to the Confederate flag that still flew in an unofficial capacity at the state capital – alongside the American and official state flags – as a persistent reminder to African Americans of the South’s history of slavery and “of systematic oppression and racial subjugation”, Obama said.

Within days after the deaths, the flag started being pulled off the virtual and real shelves of Walmart, Sears, eBay and Amazon.com, and even the gift shops of some national parks.

South Carolina Governor Nikki Haley called for its removal from the state capital, and the state of Mississippi launched a move to remove its embedded image from its official state flag.

– AAP