Information Minister Shaikh Rashid Ahmad said on Sunday that an Arab national, an important member of al-Qaida, had been arrested. He was identified as Musaad Arushi.
"The al-Qaida person is the nephew of Khalid Shaikh Muhammad," the minister said.
Khalid was the alleged mastermind of the 11 September 2001 attacks on the US and was arrested in a Pakistani army major's house in the city of Rawalpindi near Islamabad last year.
Meanwhile, Interior Minister Faisal Salih Hayat claimed an eight-member gang of foreign al-Qaida operatives had been arrested for their involvement in acts of terrorism, "including Thursday's attack on the Corps Commander's convoy in Karachi".
The eight are believed to be Uzbeks and Chechens.
The attack on the convoy of Lieutenant General Ahsan Salim Hayat killed seven soldiers, three policemen and a passer-by.
The general escaped unhurt.