The operation was launched in 2013 but it has run into troubles due to recent arrest of a close friend of former president Asif Ali Zardari, pitching his Pakistan People's Party (PPP) against ruling Pakistan Muslim League-Nawaz.
Pakistan Rangers last week arrested Dr Asim Hussain, a former minister, from Karachi and secured a 90-day remand from a court to investigate his alleged links with militants.
Since his arrest, the PPP is clamouring that the party members are being victimised by the government and security agencies.
No statement was issued about Gen Sharif's meeting with the Prime Minister but Dawn News reported that they discussed the operation in Karachi and its political implications.
The government had already made it clear that Karachi operation would go ahead against criminals and militants irrespective of their political affiliations.
According to interior ministry, crime has been reduced by about 70 per cent since launch of operation.
But the government would have to address the concerns of Zardari, whose party controls the provincial government of Sindh, of which Karachi is the capital.
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