The Karachi registry of the court, while holding a hearing on law and order in the city, cited concern at the missing containers.
The court had earlier expressed its displeasure over the free availability of sophisticated arms and ammunition in Pakistan's biggest city and financial hub.
A government commission has already investigated the matter but the bench headed by Chief Justice Iftikhar Chaudhry said that there should be a probe to ascertain how many of the missing containers had weapons.
The court further ordered law enforcement agencies to conduct door-to-door searches for illegal weapons in Karachi.
The Advocate General of Sindh requested the court to allow the provincial government to impose curfews in parts of the city where an operation would be carried out to recover illegal weapons.
The US embassy has already denied that 19,000 containers had gone missing or they were bringing in arms and ammunition for NATO forces in Afghanistan.
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