Angry Shi'ites set fire to the restaurant after the mosque attack in which five people died on Monday night, but the bodies of those burned were only found on Tuesday morning, said Rizwan Edhi of the Edhi Foundation, a private emergency service.
"We recovered the bodies of the six people from the debris of the KFC early this morning. All the dead were employees of KFC," he said.
On Monday, at least five people, including two assailants, were killed in the suicide bomb attack on the Shi'ite mosque in the same Gulshan-e-Iqbal area of Karachi.
At least 18 people were wounded, four seriously, in the attack at the Mandinatul Ilm mosque, the latest incident of religious violence to hit one of Washington's main allies in its war on terrorism.
The mosque attack came just three days after a suicide bombing at a Muslim festival in Islamabad on Friday that killed at least 19 people, most of them Shi'ite Muslims, in the worst such attack ever in the capital city.
More than 100 people have been killed in tit-for-tat attacks by majority Sunni and Shi'ite militants in the past year.
Most of the attacks have been blamed on Sunni militant groups with links to Osama bin Laden's al Qaeda network which have been angered by Pakistan's support for the war on terrorism.
Analysts say the Sunni militants have revived long standing sectarian rivalry as a means to destabilise President Pervez Musharraf's government.
Shi'ite mobs often target symbols of U.S. influence after sectarian attacks as they accuse the government of failing to act to prevent religious violence.
The attack on the KFC outlet came just minutes after attack on the Karachi mosque.
Mobs of angry Shi'ite youths also attacked a hospital, two petrol stations and burned more than a dozen vehicles.
Shi'ites make up about 15 per cent of Pakistan's mostly Sunni population of more than 150 million.
Hours before the mosque attack, unknown assailants killed a provincial leader from the Muttahida Majlis-e-Amal Islamic opposition alliance in Karachi.
Aslam Mujahid, deputy chief of Jamaat-e-Islami in the city, was kidnapped early on Monday and his bullet-riddled body was later found in an abandoned car in the east of the city.
Mairaj-ul-Huda, head of Jamaat-e-Islami's Karachi wing, said the party suspected the Muttahida Qaumi Movement, a rival regional party that is a member of the governing national coalition, of being behind the killing.
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