"We had been given some information by the government of Iran," foreign office spokesman Masood Khan said at his weekly news briefing.
"The information that was shared with us pointed to certain individuals and we had to hold these debriefing sessions," he said.
The International Atomic Energy Agency (IAEA) also "approached" Pakistan which led to "debriefing" of a few scientists, he said.
Local media reported this month that Yasin Chohan and Farooq Mohammad, directors of the country's key facility of Kahuta Research Laboratory (KRL), were taken from their homes in early December for questioning.
Chohan has since returned home but Mohammad Farooq is still being questioned.
Khan said the creator of Pakistan's nuclear bomb, Abdul Qadeer Khan, had also been questioned but denied reports that the government had placed unspecified restrictions on him.
"No restrictions have been imposed on him," he said.
However, "questions are being asked from Qadeer Khan with regard to debriefing sessions," he said.
The New York Times reported Monday that information Iran turned over to the IAES two months ago had strengthened suspicions that Pakistan sold key nuclear secrets to Iran.
But Khan reiterated that the government of Pakistan had never authorized or initiated any transfers of sensitive nuclear technology to any country.
"Pakistan has never proliferated and will never proliferate.
"The president of Pakistan has given his 400 percent assurance and commitment that no violation of Pakistan's commitment will ever take place," he said.
Pakistan has a "very strong command and control system and a very stringent export control regime. There should be no doubt about it," he said.
"Pakistan takes its responsibility as a nuclear weapons state very seriously. Since a strict command and control system was established, nothing of the sort has happened."
Khan said Pakistan had taken a "proactive approach" by interviewing the scientists and if at the end of debriefing sessions it found the individuals were responsible for passing on nuclear information, it would act against them under the law.
"If they are found responsible at the end of debriefing sessions, we shall take action against such individuals if warranted and if they are found culpable under our laws. Nobody is above the law."
He also denied reports that officials of other countries were involved in questioning Pakistani scientists.
"These are purely in-house investigations. No foreigners or foreign agencies are associated with the debriefing sessions."