Afghanistan's interior ministry said on Sunday one of its employees is suspected of shooting dead two U.S. officers inside its headquarters a day earlier, an attack that prompted NATO to recall all its staff from ministries.

An employee has been identified as a suspect and he has now fled. The interior ministry is trying to arrest the suspected individual, it said in a statement.

Afghan security sources identified Abdul Saboor, a 25-year-old police intelligence officer, as a suspect in the shooting of the Americans at close range deep inside the interior ministry.

The killings at a key security arm of the Afghan government are bound to raise fresh questions about the effectiveness of Afghan security forces as NATO combat forces prepare to withdraw by end-2014.

NATO is supposed to be moving away from a combat role to an advise-and-assist mission as early as next year. That will require NATO to place more staff in Kabul's ministries.

The attack took place on Saturday as rage gripped the country for a fifth straight day over the burning of the Muslim holy book at a NATO base, despite an apology from U.S. President Barack Obama.

Riots erupted again in Afghanistan on Sunday, Reuters witnesses said, with thousands in northern provinces hoisting the white Taliban flag and throwing stones at police, who fired into the air to disperse the crowds.

But unlike earlier protests last week, which killed 29 people and wounded 200, including two U.S. troops killed by an Afghan soldier, there were no reports of violence.

CCTV footage showed that Saboor had access to the Command and Control Centre, tucked deep inside the ministry, where the slain Americans were found, security officials told Reuters on condition of anonymity.

The Taliban took responsibility for the attack, saying it was in retaliation for the burning of the Korans.

The Koran burnings have underscored the deep cultural mistrust between Afghans and the foreign troops who invaded a decade ago to oust the Taliban from power.

Afghan President Hamid Karzai repeated his plea for calm and restraint. It is time to regain and preserve our calm, and not allow our enemies to misuse it, he told reporters, referring to the nationwide violence.

(Writing by Amie Ferris-Rotman; Editing by Michael Georgy and Ed Lane)