The South Carolina Senate has voted on a bill to remove the Confederate flag from the State House grounds and place it instead in a Confederate relic room for display.

State senators passed Senate Bill 897 on second reading with a 37-3 vote on Monday, weeks after the shootings at Emanuel African Methodist Episcopal Church in Charleston, South Carolina, that left nine people dead.

The bill will amend South Carolina's 1976 Code, which authorised flags that would be flown atop the State House and on the Capitol grounds.

It aims to "remove references to the South Carolina Infantry battle flag of the Conderate States of America."

If the bill is passed by the House and signed by the governor, the only flags that will fly on the Capitol grounds are the American flag and the South Carolina State flag.

South Carolina Gov. Nikki Haley, who earlier said she wanted to remove the Confederate flag, praised the Senate for the "historic occasion" of voting for the bill.

"I applaud the Senate's decisive action, look forward to the Senate giving the bill third reading in the morning, and ask that the House act swiftly and follow the Senate's lead," she posted on Facebook.

During the Senate session on Monday, senators praised Senator Clementa Pinckney, who was one of the nine killed by Dylann Roof last June 17.

"The one thing you can say about Senator Pinckney is basically true is that he had a good heart. Senator Pinckney in his years of service in the House and the Senate, as a pastor, as a community leader and as a friend leaves much evidence. So the challenge to those of us as we yet live is to leave some evidence that we live and that we serve," said Senator John Matthews Jr.

Republican Senator George Campsen said in responding to the church shootings, "let us not focus upon what outsiders say."

"Let us focus upon us, the relationships in our communities and State. If the confederate flag on our State House grounds upsets a significant number of citizens, let's remove it in the name of peace and mutual upbuilding," he said.

The state Senate on Monday rejected amendments that would fly the flag on Confederate Memorial Day and the other one that would allow the public to vote on whether to remove the flag, according to a Reuters report.

Republican State Senator Lee Bright, who suggested the popular vote, said, "I'm more against taking it down in this environment than any other time just because I believe we're placing the blame of what one deranged lunatic did on the people that hold their Southern heritage high."

A survey among South Carolina lawmakers on how they would vote after Haley called for the removal of the flag showed 33 senators and 83 House members agreeing with her.

Democrats said they cannot support any flag linked to the Confederacy, which Haley and business leaders agreed.

"There is no good-looking Confederate flag. It all stands for the same thing — secession," according to Lonnie Randolph, president of the South Carolina chapter of the National Association for the Advancement of Coloured People.