"There is a great danger till the 10th of Muharram," Malik said during an interaction with reporters in Islamabad.
He said authorities in the four provinces had been directed to ensure that no motorcycles were parked within half a kilometre of imambargahs.
Cars too should be parked a kilometre away from the Shia prayer halls, he said.
Three persons were killed and over 20 injured, including five Pakistan Rangers personnel, when a bomb attached to a motorcycle went off outside an imambargah in Karachi late last night.
A 'majlis' or religious gathering was underway at the prayer hall at the time of the blast.
Malik claimed the attack in Karachi was not of a sectarian nature but had been carried out by a "third group".
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He did not give details in this regard.
He further said he would continue to work to curb terrorism despite criticism he was facing for blocking mobile phone services and riding of motorcycles in the past few weeks.
These bans were imposed because of information received from intelligence agencies regarding terrorist attacks using mobile phones and motorcycles in Karachi and Quetta, he claimed.
Karachi and Quetta were being targeted to attain "specific objectives", he said without giving details.