Rashid told a private TV channel said the security men on a tip raided a house in Quetta, two days ago and arrested the suspect after shootout.
He said identification of the dead and arrested have yet to be established. However he said the man arrested may be Mustafa Setmarian Nasar, who has allegedly played important role in the March 11, 2004, Madrid bombings that left 191 people dead and more than 1,500.
Meanwhile, a senior security official in Balochistan said that one local Saboor was killed, who was the relative of a local mayor.
"The investigation is going on to know what relations the local had with al Qaeda suspect," the official said.
The security men conducted the raid without police as they wanted to keep it highly secret, the official said.
Reports suggest that Saboor belonged to a banned outfit Jaish-e-Mohammed, but there is no official confirmation of the report.
Government says it has arrested more than 700 al Qaeda suspects and Taleban since the military operation launched in Afghanistan in October 2001.