"We basically seek permission to see Dr Qadeer Khan and investigate into the matter as well as restrain him from making any statement and interacting with anybody," Naveed Inayat Malik told the Reuters news agency.
The newspaper published excerpts of what it said was Khan's official account of his country's dealings with Iran, that describe the Islamic state's attempted purchase of nuclear weapons in a $10bn deal.
The deals allegedly occurred with the knowledge of the Pakistani government - but Islamabad and Khan have denied the reports.
Malik said the Lahore high court would hold a preliminary hearing on the matter later on Monday.
Khan was at the centre of the world's biggest nuclear proliferation scandal in 2004 when he confessed to selling nuclear secrets to Iran, North Korea and Libya.
Pakistan, which has not signed the nuclear Non-Proliferation Treaty, conducted several nuclear tests in 1998 but is thought to have the capability to produce bombs since 1986.
Pakistan hopes to bring up the subject of a civilian nuclear deal with the US at this week's strategic dialogue in Washington.
There have been signs of a softening of Washington's stance on the subject, especially given Pakistan's chronic and severe power shortages leading to hours without electricity every day across much of the country.
It is unclear how the new allegations against Khan might affect any deal.