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An American Muslim civil rights group has slammed US President Donald Trump's choice of interim National Security Advisor (CAIR) following the dismissal of John Bolton earlier this week.

The Council on American Islamic Relations said it was "appalled" at the choice of Charles Kupperman due to his association with anti-Muslim groups.

"While we welcome the resignation of John Bolton, who has a long track record of promoting anti-Muslim policies and associating with hate groups, we cannot simply replace one Islamophobe with another," CAIR Executive Director Nihad Awad said on Wednesday.

Kupperman, who is accused of being a right-wing extremist, had previously served on the board of the Center for Security Police - a group described by the Southern Poverty Law Center as a "conspiracy-oriented mouthpiece for the growing anti-Muslim movement".

The CSP and its founder, Frank Gaffney, have peddled a number of conspiracy theories, including one that alleges the Muslim Brotherhood has infiltrated the US government.

Kupperman was a member of CSP's board from 2001 to 2011.

Former National Security Advisor Bolton - a known Iran hawk left his position this week, reportedly due to the president's interest in securing talks with his Iranian counterpart.

Iranian President Hassan Rouhani signalled his approval of Bolton's dismissal on Wednesday by urging Trump to "put warmongers aside" as Tehran and Washington remain locked in the crisis that unfolded following the Trump administration's withdrawal from the landmark 2015 nuclear accord with Iran.

It is expected that Kupperman, who was hired by Bolton earlier this year, will soon be replaced by a permanent office holder. Kupperman and Bolton are believed to be in agreement on many of the key policy areas which the former National Security Advisor diverged with Trump on.