A three-judge bench headed by Chief Justice Iftikhar Chaudhry ordered Ali Musa Gilani and Principal Secretary Khusnood Lashari to record their statements with the Anti-Narcotics Force (ANF) before the next hearing on April 20.
Ali Musa Gilani was recently elected a member of the National Assembly or lower house of parliament in a bye-election in Multan.
Earlier, the premier's elder son, Abdul Qadir Gilani, was linked to alleged corruption in the arrangement of the Haj pilgrimage in 2010.
The apex court is examining allegations about out-of-turn quotas for importing raw materials that were granted to two pharmaceutical companies by the Health Ministry, allegedly under the influence of Ali Musa Gilani.
ANF officials have informed the court that quotas for 9,000 kg were granted to Berlex Labs International and Denis Pharmaceutical though the official limit for Ephedrine is 500 kg.
The International Narcotics Control Board fixed an annual quota of 22,000 kg of Ephedrine for Pakistan for 2010-11 but the Health Ministry allegedly allocated quotas for around 31,000 kg.
Lashari was the Health Secretary when the quotas were allotted.
Following media reports yesterday that the government had transferred two officials who were investigating the Rs 7 billion scam, the apex court on Tuesday ordered that the officials should be allowed to continue the probe.
The Chief Justice referred to the reported transfer of the officials and remarked that this may have happened as some prominent persons were involved in the scam.
One of the officials, Brig Faheem Ahmed Khan, told the bench that the ANF had earlier issued summons to Ali Musa Gilani and Lashari to record their statements last year.
At Lashari's request, ANF officers met him at the Prime Minister's House and Lashari reportedly said the premier was upset at the summons issued to his son, Khan told the court.
Khan further told the court on Tuesday Narcotics Control Board chief Zafar Abbas had stopped his team from carrying on further investigations.
The apex court last month turned down a request from authorities to close the case.
The issue was earlier raised in the National Assembly in 2009 and former Health Minister Makdoom Shahabuddin had set up a fact-finding committee.
On the recommendation of this committee, the ANF had initiated an investigation.