City police chief Shahid Hayat confirmed the killings saying five members of the Shiite community were shot dead in several districts.
A doctor was shot dead in Manghopir neighbourhood in western district and another was gunned down around noon at Tariq Road in the eastern part of the city.
They were identified by police as Dr Sher Ali and Dr Naseem Zaidi.
"The killing pattern shows that they were apparently carried out on sectarian grounds," Javed Alam Odho, the deputy inspector general of police told AFP.
The other two victims were killed in central district when unknown attackers burst into a tailor's shop and opened fire.
The owner and a worker were killed and three others were injured.
"The attack seemed to be on sectarian lines as all of the people inside the shop were Shiites," senior police officer Aamir Farooqi said.
The fifth killing took place in Gulshane Iqbal town where a Shiite youth was shot dead by gunmen riding a motorbike, Pir Mohammad Shah, a senior police officer told AFP.
Majlise Wahdatul Muslimeen (MWM), an alliance of Shiite Muslim groups held protest rallies and sit-ins in different parts of Karachi to condemn the killings.
The latest attacks came ahead of the beginning of the Muslim holy month of Moharram, when Shiites mourn the seventh century martyrdom of Hussain, the grandson of prophet Mohammad, along with his family members (PBUT).
Shiites make up around a fifth of Pakistan's predominantly Sunni Muslim population.
Police are already carrying out operations against criminal groups to curb sectarian and political killings.
Security would be further tightened in the month of Moharram, they said.
"We are already carrying out the operation against sectarian and other elements and we would certainly intensify our efforts during the coming days," Odho said.
Karachi, a city of 18 million people which contributes 42 percent of Pakistan's GDP, is rife with murder and kidnappings and has been plagued for years by ethnic, sectarian and political violence.
Four Shiite Muslims martyred in grenade attacks in northwest Pakistan two days ago