The attacker blew himself up near a police checkpoint located less than a kilometer from the Pakistan army headquarters and office of President Pervez Musharraf, who was unhurt.
Three policemen and three passers by died, and more than 20 people were injured, media said.
No one has yet taken responsibility for the attack.
The blast came almost two weeks after another attack in Karachi left 140 people dead and over 500 injured, after two explosions in the middle of a huge crowd near the motorcade of ex-premier Benazir Bhutto, who had returned to the country after eight years of self-imposed exile in Dubai.
Musharraf, 64, seized power in a bloodless military coup in 1999. On October 6, he won the country's presidential elections despite protests by opposition parties claiming that Musharraf, as the Armed Forces commander in chief, was not entitled to run for president.
The Supreme Court has yet to announce the official election results and the country is currently ruled by an interim government until parliamentary elections slated for January next year.
