The Libyan militia leader charged over a deadly attack on the US mission in Benghazi pleaded not guilty during a brief appearance in US federal court on Saturday.

A federal grand jury indicted Ahmed Abu Khatallah during the rare Saturday session on a single charge of conspiracy to provide material support and resources to terrorists for the attacks that killed US ambassador Chris Stevens and three other Americans on Sept 11, 2012.

He was flown to Washington by helicopter shortly after sunrise from a US navy warship where he had been held and interrogated since his high-profile capture two weeks ago, a law enforcement official.

The suspect, believed to be 43 and also known as Ahmed Mukatallah, listened to the court proceedings through an interpreter and raised his right hand before his court - appointed lawyer, Michele Peterson, entered a not-guilty plea on his behalf.

The case's lead prosecutor warned that the US Justice Department could bring additional charges against Abu Khatallah during the ongoing investigation about the assault that saw gunmen storm the US mission in Benghazi and set it on fire.

Abu Khatallah is due back in court, located just 1.6 km from the White House, on Wednesday for a detention hearing, and again on July 8 for a status hearing.

The US State Department has identified Khatallah as a senior leader of Ansar al-Sharia, a Libyan group responsible for a spate of attacks and assassinations.

The case relies heavily on accounts from Libyan officials and witnesses who have singled out Khatallah as taking part in the assault that day.

FBI investigators were only able to visit the crime scenes to collect evidence several weeks after the assault due to high security concerns.

Libya accused Washington of violating its sovereignty, though it had failed to fulfill an outstanding arrest warrant against Abu Khatallah because of the tense security situation in the flashpoint eastern city of Benghazi.

The raid represents a victory for US President Barack Obama, who has faced intense criticism over his administration's handling of the Benghazi assault and its aftermath.

Some Republicans have criticized the administration's decision to try Khatallah in civilian court rather than through the Guantanamo Bay special military tribunals.

Republican Senator Kelly Ayotte expressed "serious concerns that conducting a rushed interrogation onboard a ship and then turning Khattalah over to our civilian courts risks losing critical intelligence that could lead us to other terrorists or prevent future attacks".

The Benghazi attack raised questions about security at US diplomatic facilities worldwide and the accuracy of US intelligence on militant threats.

Republicans charged that the White House failed to respond decisively and then tried to hide some facts in the grisly episode.

The Obama administration, in turn, has accused critics of politicizing a tragic event.