Law enforcement agencies after a tip off about presence of militants raided Gulshan-e-Buner area of the city, leading to heavy exchange of fire.
A police official said that five militants including a Taliban commander were killed in the operation.
"Police also recovered weapons and bomb making material from the slain militants," he said.
Pakistan government asked paramilitary Rangers and police in September to launch operations against the militants and criminals in Karachi, the financial hub of the country.
The banned militant and criminal groups also regularly attack the police and Rangers in retaliation.
According to a police report, so far 91 police and nine Rangers personnel have been killed this year in targeted attacks.