The online payment company PayPal appeared on Saturday to have disabled the account of the Council of Conservative Citizens (CofCC), a rightwing organization that was cited in a manifesto linked to the South Carolina shooting suspect Dylann Roof and has given to prominent Republican politicians.

Attempts to donate to the organization, which Roof apparently credited in an online manifesto with having informed his white supremacist views, result in a message that “this recipient is currently unable to receive money”.

Roof faces charges of murder over the deaths of nine people, all African American, at a Bible study group at the Emanuel AME Church in Charleston on 17 June.

On Saturday, representatives for PayPal did not immediately respond to questions. A former spokesman for the CofCC, Jared Taylor, said he “had no idea” about the status of the organization’s account.

Earl Holt, the leader of the CofCC, has given more than $60,000 to Republican campaign funds. Four Republican hopefuls for president this week promised to return money given by Holt, after the Guardian approached them about the donations.

The Southern Poverty Law Center (SPLC), a legal advocacy group, reported PayPal’s apparent action on Saturday. The group has campaigned for PayPal to suspend the CofCC and dozens of other organizations it characterizes as hate groups.

The SPLC describes the CofCC as “a crudely white supremacist group” and notes that its website regularly condemns “race-mixing” and disseminates stories of “a victimized white majority under siege by allegedly violent people of color”.

PayPal maintains that it does not allow donations to websites that violate the company’s “offensive materials policy”, which “prohibits individuals and groups from making a call to action for violence of any sort against any group, promoting or glorifying hate, violence or racial intolerance or graphically portraying violence or the victims of violence”.

Online remarks that were made in Holt’s name included inflammatory assertions such as a description of black people being “the laziest, stupidest and most criminally-inclined race in the history of the world”. On Saturday the rightwing website theblaze.com, on which many such remarks were made, appeared to have suspended the user in question.

Stories on the CofCC website often include graphic photos and feature headlines such as “Entire family attacked in racially motivated lynching in Alabama” and “Black power militants descend on McKinley, Texas”. The posts do not include bylines but are likely the work of webmaster Kyle Rogers, Keegan Hankes, a research analyst with the SPLC, told the Guardian.

Rogers also runs a flag business where bestselling items include a “Southern Nationalist” flag and the Confederate flag. The latter, properly referred to as the Army of Northern Virginia Battleflag, is at the centre of ongoing controversy around the Charleston shootings. On Saturday it was removed by an activist from the grounds of the South Carolina statehouse. The activist and a helper were arrested and the flag raised again.

The flag company’s site also uses PayPal. By Saturday afternoon its account had not been disabled.

Hankes said it appeared that the murder of nine black people in Charleston and subsequent media stories about the CofCC had prompted PayPal’s action, but acknowledged that the company likely would not confirm a suspension due to privacy concerns.

“It’s a shame that it took a tragedy for them to take action,” Hankes said. “This is a good first step, but they’ve got a lot of work ahead of them.”

Hankes said PayPal was essentially “the banking system of the radical right movement”.

“They probably don’t make very much money off it, because it’s a very small community of people, numbers-wise,” he said, “but any amount of money goes a long way for them.”

In a statement issued last week, Holt said it was “not surprising” that Roof had apparently taken to his group’s website, but added: “The CofCC is hardly responsible for the actions of this deranged individual merely because he gleaned accurate information from our website.”