The two separate trips preceded the current probe into 13 top nuclear scientists, engineers and administrators, including the revered "father" of Pakistan's nuclear bomb Abdul Qadeer Khan.
The inquiry trips were prompted by a letter in November from the UN's nuclear watchdog, the International Atomic Energy Agency (IAEA), Information Minister Sheikh Rashid said.
"After the IAEA inquiries they wanted to have themselves some information against some people," Rashid said of the Pakistani team.
The IAEA letter came after almost a year of US media reports quoting unnamed US, European and Middle East officials accusing Pakistan of being the source of leakages of nuclear weapons technology to Iran, North Korea and more recently Libya.
Rashid said he did not know who was in the team or how large it was.
"They wanted to check how much involved (the scientists and engineers) were, whether they were involved or not."
Asked what they were alleged to be involved in, Rashid said: "something like information leakage."
Rashid would not say when the trip took place, but it appears to have been between the receipt of the IAEA letter in November and the first interrogations of nuclear scientists in December.
Four scientists, including Mohammad Farooq, the director of Pakistan's key uranium enrichment plant A.Q. Khan Research Laboratories, were taken in for questioning in December. Another eight were taken in at the weekend.
Even Khan himself, an official national hero, was also questioned though not in custody.
A senior government official, who requested anonymity, said investigators first went to Vienna, Austria, where the IAEA is headquartered.
"Pakistan sent a small team of technical officials first to Vienna, then to Iran after which they launched the debriefing of four scientists in the first week of December," the official told AFP.
"In late December another team comprising more or less the same number of officials visited Tripoli and in the light of their finding the second round of debriefing was started."
He said the investigation was focussed on "a particular group of people" who worked at KRL, stressing it was "not against all nuclear scientists or officials."
Most of the officials undergoing debriefing have already retired from KRL, he added.
Three of those held in custody have since been cleared and released, Rashid announced Wednesday night.
The Pakistani government, which has always vehemently denied any proliferation, admitted for the first time in December it admitted that individual scientists were under suspicion.
Islamabad officials however insist any proliferation would only have been on an individual basis for "personal greed or ambition," and insists no government entity ever sold nuclear knowledge.
Iran and Libya are on the United States' list of "rogue states" that allegedly support terrorism.
The New York Times reported early January that Pakistan appeared to be the source of uranium centrifuge design technology that helped Libya make big strides in its nuclear program in the past two years.
The transfer of Pakistani designs made it possible for Libya to make "major strides" in enriching uranium for use in nuclear weapons, the paper said, quoting unnamed Washington officials and other Western experts.