Opposition politicians and Pakistani media said on Thursday that Faruq Muhammad, director of Pakistan's key uranium enrichment facility Kahuta Research Laboratories (KRL), and a KRL laboratory director, Yasin Chohan, were arrested this month.
"They have been arrested and are under detention," opposition senator Ishaq Dar, of the Pakistan Muslim League-Nawaz (PML-N) party, said on Thursday.
"I say this with full responsibility on the basis of credible information."
Urdu-language newspaper Jinnah reported that Caucasian men wearing bullet-proof jackets had arrested Faruq at his home in Rawalpindi, near Islamabad. It said Chohan was also taken from his home.
A government spokesman refused to confirm whether the two men were in detention. A foreign ministry statement said nuclear scientists routinely underwent "personnel dependability and debriefing programmes".
The statement added: "The matter referred to falls within the scope of such programmes."
"The detention of the two nuclear scientists shows Musharraf wants to perpetuate his rule by pleasing foreign powers. He has crossed all limits to disgrace, humiliate and surrender on national interests"
Faruq's daughter refused to discuss her father's whereabouts when contacted.
"No comment," she replied, declining to give her name. "The family is fine and there is nothing for us to worry about."
However, the government rejected media reports that the two men were connected to alleged transfers of nuclear technology to Iran.
"There are reports about many sources from where Iran could have obtained nuclear technology, including several Western companies and individuals. The focus should be on checking out with those sources," the foreign ministry said.
The PML-N party said it believed the two men were being held by US Federal Bureau of Investigation (FBI) agents.
"According to our information, the FBI is holding Director General Dr Faruq and Laboratory Director Yasin Chohan with the assistance of Pakistani agencies," said a party statement, condemning the arrests.
At a press conference late on Thursday the PML-N accused President Pervez Musharraf of allowing foreigners to arrest Pakistan's most prized government employees.
"The detention of the two nuclear scientists shows Musharraf wants to perpetuate his rule by pleasing foreign powers. He has crossed all limits to disgrace, humiliate and surrender on national interests," PML-N chief coordinator Ahsan Iqbal said.
"This kind of action will only support the cause of those elements who think the American war against terrorism is in fact a war against Muslims."
Musharraf has been accused of
being too close to the US
The PML-N aslo raised concerns that the architect of Pakistan's nuclear programme, Abd al-Qadir Khan, may also come under future arrest.
Khan, who founded KRL, has been named in international media reports which claim that Pakistan aided both Iran's and North Korea's nuclear programmes.
KRL was sanctioned by the United States in March for allegedly helping an unnamed foreign country or entity to develop weapons of mass destruction.
Islamabad, which went public as a nuclear power in May 1998 when it conducted underground nuclear tests, consistently denies reports of exporting nuclear know-how.