In the southern American city of Charleston, at least one black church will post a look-out on Sunday to warn those inside if a white stranger approaches.
Twenty-one year old Dylann Roof has been arrested over the shooting of nine people at a bible study group at an historic African-American church.
Witnesses said he walked into the building and sat there for some time before opening fire.
Local reporter Paul Bowers told Checkpoint it was not clear when the church would re-open.
Prayers held across US
Prayers have been held across the United States after the killings in Charleston.
Six women and three men, including the pastor, died in the attack. A hate crimes investigation has been launched.
Several churches in Charleston were full to overflowing today as prayer services were held. Some services were held outdoors.
Outside the Emanuel AME Church, where the attack took place, hundreds gathered in soaring heat to pay tribute.
"We really have to fight together to go on and to live a civilised life where race doesn't matter," said one woman, Martha Watson.
At a vigil for victim Sharonda Singleton, her teenage children told the BBC they had forgiven the killer and wanted to focus on moving on in a positive way.
Services were held in several other cities, including Miami, Detroit and Philadelphia.
In New York, services and protests took place, with placards including such messages as "Black Lives Matter" and "Stop killing black people".
Richard Price, executive assistant at the Harlem Church of Christ, said: "That someone would come and infiltrate that sacred space, one of the only spaces we ever really have, and to violate that space, and then to shoot the place up...
"This is a deep, deep-seated hurt that may never ever heal."
Suspect given gun for birthday
Dylann Roof had recently been given a weapon as a birthday present, according to a relative.
The 21-year-old's uncle told Reuters that Mr Roof's father gave him a .45-calibre handgun.
Carson Cowles said he tried to mentor his nephew, who had no job or driver's licence, but Roof was not receptive to the idea.
"I actually talked to him on the phone briefly for just a few moments and he was saying 'well I'm outside target practising with my new gun'," Mr Cowles said, describing a phone call around the time of Mr Roof's birthday in April.
Mr Roof's jacket in a photo on his profile page prominently bears the flags of South Africa and Rhodesia, now Zimbabwe, from when the African nations were ruled by the countries' white minorities.
The president of Southern Poverty Law Center (SPLC) in Montgomery, Alabama, Richard Cohen said it was unclear whether Roof was connected to any of the 16 white supremacist organisations SPLC had identified as operating in South Carolina.
But Mr Cohen said Mr Roof appeared to be a "disaffected white supremacist" based on his Facebook page.
Police identified Mr Roof after receiving tip-offs from friends and family who claimed to recognise him in surveillance footage from the church.
The suspect was detained during a traffic stop in Shelby, North Carolina.
US President Barack Obama said he and his wife had known several members of the Emanuel AME Church, including pastor Clementa Pinckney.
Mr Obama raised the issue of gun ownership, saying: "At some point, we as a country have to reckon with the fact that this type of massacre does not happen in other advanced countries".
Presidential candidate Hillary Rodham Clinton said the US had to face "hard truths" on guns.
"How many innocent people in our country, from little children to church members to movie theatre attendees, how many people do we need to see cut down before we act?"
- BBC / Reuters