Chaudhry is heading a three-judge bench that has taken suo motu notice of the murder of 20-year-old Shahzeb Khan, the son of a senior police officer who was shot dead in Karachi in December.
The prime suspect, Shahrukh Jatoi, 20, flew to the United Arab Emirates from Karachi, without any record of his departure despite an alert for his arrest.
"Two months have passed and nobody knows how Shahrukh Jatoi managed to escape...If this is the state of affairs of security agencies at airports, then tomorrow, terrorists might escape after carrying out attacks," the Chief Justice said.
Jatoi returned to Pakistan last month to face trial but the apex court has directed authorities to punish those who allowed him to fly out of the country.
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During today's hearing, the bench directed a lower court to conduct the trial of Jatoi on a daily basis.
The Chief Justice remarked that the crime rate in Karachi was increasing and the issue should be tackled with an iron hand.
Police officials said they had examined CCTV footage provided by airport security but found no record of Jatoi.
"If a young boy can deceive you, then how can you stop terrorists?" the Chief Justice said.
The bench observed that action should be taken against police and FIA officials involved in Jatoi's escape from the country.
The bench directed authorities to submit an explanation for lack of progress in the case and adjourned the matter for 10 days.