"The debriefing session of one of the scientists has concluded and he has resumed his normal duties," foreign ministry spokesman Masood Khan told AFP on Friday.
Local newspapers had linked the pair's apparent detention to allegations that Pakistani scientists helped Iran develop its alleged nuclear weapons programmes.
Yasin Chohan, a laboratory director at the Kahuta Research Laboratories (KRL) uranium enrichment facility, returned home on Friday morning, an associate of Chohan's family told reporters.
Chohan and KRL director Farooq Muhammad were taken from their homes in early December and held for questioning, according to opposition politicians and local news reports.
Pakistani officials denied the pair were in custody, saying they were merely undergoing "personnel dependability and debriefing programmes."
Foreign ministry spokesman Masood Khan also denied the men were being interrogated or were in custody, or that any foreigners were involved.
"There is no 'interrogation' going on. The word has implications of 'wrongdoing'. This is prejudgement," Khan told reporters.
Pakistan owns missiles capable
of carrying a nuclear warhead
"People in debriefing sessions are not held in 'custody'." Khan said the scientists had also been undergoing "personnel
But he declined to answer whether the men had freedom of movement.
Opposition parties are furious at the scientists' detention and have accused President Pervez Musharraf of trying to appease the United States.
Also on Friday, Pakistan's central bank froze the accounts of three more Islamic groups banned last month.
Pakistan's President Pervez Musharraf, a key ally in the US-led "war on terror", outlawed six Islamic groups last month after Washington raised concerns about the re-emergence of the armed Islamist groups within the country.
But it has taken several weeks for the interior ministry to notify the central bank to freeze the groups' accounts, allowing their members plenty of time to withdraw any money.
Three groups had their accounts frozen last week. On Friday
the State Bank of Pakistan moved against Jamiat al-Ansar, Hizb al-Tahrir and Jamiat al-Furqan.
A police official in Karachi commented: "The action will have no impact because it is too late."