An international press freedom organisation has called for an independent investigation into the killing of a journalist in Egypt.

Reporters Without Borders also expressed "deep concern" at the continued detention of journalists on terrorism charges.

Mayada Ashraf, a reporter for Dostour newspaper and Masr Al-Arabiya news website, was shot in the head while covering clashes between Muslim Brotherhood supporters and police in Cairo on Friday.

The group said it was “dismayed” by Ashraf’s death and concluded that journalists in Egypt have been “systematically targeted” since the ouster of Islamist president Mohamed Morsi in July 2013.

It is not clear who shot Ashraf as protesters and security forces have both been accused of using live ammunition during the clashes.

“We offer our heartfelt condolences to Ashraf’s family and colleagues and we urge the competent authorities to carry out an independent and impartial investigation to ensure that this crime does not go unpunished,” said Lucie Morillon, head of research and advocacy at the France-based group.

Political polarisation and instability have rocked Egypt since Morsi's ouster.

The latest clashes came after Field Marshal Abdel-Fattah El-Sisi resigned from his post as army chief and defence minister to run for president in elections due in May.

Ashraf is the eleventh journalist to be killed while doing their job since January 2011, and the sixth since 3 July 2013, the group said.

It also expressed concern at the fate of journalists “arbitrarily detained” in Egypt.

Twenty people -- nine of whom are Al Jazeera journalists -- are on trial for "airing false news or joining a terrorist organisation" -- a reference to the Brotherhood, which was officially designated by Cairo a terrorist group late last year.

Three of the defendants, Al Jazeera English journalists Peter Greste, Mohamed Fahmy and Baher Mohamed, have been in custody since late December.

The court recently adjourned their trial for the fourth time, to 10 April, and denied them bail for the second time.

“The authorities must stop invoking the fight against terrorism in order to persecute dissident journalists,” Morillon said.

“We call on them to release all journalists who are being held on spurious grounds and to withdraw the proceedings against them. We also urge them to respect the newly adopted constitution as well as Egypt’s international obligations as regards freedom of information.”

The group mentioned other journalists on trial, including Abdullah El-Shami, who has been held since 14 August “without any charge being brought against him.”

Several employees of the Rassd news network, known to report in favour of the Brotherhood, are facing military trials, the rights group noted.

The interim authorities designated the Brotherhood a terrorist organisation in December 2013, blaming it and its allies for attacks in the Sinai Peninsula, Nile Delta and Cairo.

Egypt is ranked 159th out of 180 countries in the 2014 Reporters Without Borders press freedom index.