The country's Information Minister Sheikh Rashid said the probe was under way after the United Nation's nuclear watchdog sent a letter in November raising fears of proliferation.
"Following reports from the International Atomic Energy Agency (IAEA), we sent our own team to Iran, Libya and Vienna and after that we started the debriefing sessions," the minister said on Wednesday.
He was referring to a surprise investigation by Islamabad on 12 Pakistani nuclear scientists and administrators associated with its key uranium enrichment facility, Khan Research Laboratories.
Several nuclear scientists have since been taken into government custody for questioning.
"Now there are a total of nine scientists and officials who are currently undergoing debriefing," the minister said.
The letter from the UN concerned the suspected involvement of Pakistani scientists and officials in trading nuclear know-how for cash.
Rashid said anyone found guilty of indulging in nuclear leaks would be punished.
"As a responsible nuclear state we cannot let any individual of sensitive organisations violate the rules and bring a bad name to the country"
"As a responsible nuclear state we cannot let any individual of sensitive organisations violate the rules and bring a bad name to the country," he said.
The investigation was expected to be over by next week. The minister said none of those questioned would be handed over to the United States.
Pakistan had consistently denied any leak of its nuclear technology until December, when it admitted that it was questioning several scientists.
The country joined the nuclear club in May 1998 when it conducted underground nuclear tests in response to similar tests by India.