The calls came after the government revealed that several scientists had been questioned about the spread of sensitive technology to Iran in response to information from Tehran and the International Atomic Energy Agency.
"It should be thoroughly probed how our scientists, who are trusted so well and watched so closely, are named," former air marshall Ayaz Ahmed said.
"We should get into the bottom of the issue and the enquiry report should be made public. When we make a mistake we better acknowledge it," he told AFP.
Pakistan said Tuesday it had placed some senior nuclear scientists under investigation because of information they may have cooperated with Iran's nuclear programme for "personal ambition or greed".
"We are investigating individuals who might have violated Pakistani law for their commercial gains," Foreign office spokesman Masood Khan said Tuesday.
The authorities earlier this month took in Farooq Mohammad and Yasin Chohan, directors of Pakistan's key uranium enrichment facility Kahuta Research Laboratories (KRL), for questioning.
The government spokesman said the father of the country's nuclear programme and former KRL chairman, Abdul Qadeer Khan, had also been questioned.
However, he denied the movements of Khan, who is revered as a national hero, had been restricted.
Qadeer Khan appeared as a chief guest at a seminar on science and technology for socio-economic development in Islamic states late Wednesday.
The scientist, who was given a standing ovation by the audience, declined to answer a volley of questions on the debriefing of nuclear scientists.
"No comments," he told reporters before leaving in an official black Sedan.
"Doctor Qadeer Khan has faced many ups and downs in his life and he is facing some now. Let's not be daunted by all these things," minister for science and technology Atta-ur Rehman said in his speech.
The New York Times reported Monday that information Iran turned over to the IAEA two months ago had strengthened suspicions that Pakistan sold key nuclear secrets to Iran.
Pakistan's suspected role in providing centrifuge designs to Iran was also revealed by the Washington Post, which said the blueprints provided a "tremendous boost" to Iran's pursuit of nuclear weapons.
Centrifuges can be used to enrich uranium, or spin it at supersonic speeds to produce a concentrated material used to make nuclear weapons.
Defence analyst Air Marshal Ahmed said any inquiry should not be one-sided and that the scientists should be given the opportunity to tell the truth.
Former lieutenant general Kamal Matinuddin said he had doubts about the reports from Iran.
"We have a strong command and control system. Pakistan has repeatedly said we are not at all involved in any transfer of technology," Matinuddin said.
Government spokesman Masood Khan stressed that "other countries and individuals in Europe, Asia and North America have also been named. They should also be investigated. Pakistan should not be singled out."
Islamabad, which went public as a nuclear power in May 1998 when it conducted underground nuclear tests, has consistently denied reports that it has exported its nuclear know-how.
President Pervez Musharraf has rejected the allegations as a smear campaign.
"The president of Pakistan has given his 400 percent assurance and commitment that no violation of Pakistan's commitment will ever take place," said government spokesman Khan.