"The debriefing session of one of the scientists has concluded and he has resumed his normal duties," foreign ministry spokesman Masood Khan told AFP.
Local newspapers had linked the pair's apparent detention to allegations that Pakistani scientists helped Iran develop its nuclear programs.
Yasin Chohan, a laboratory director at the Kahuta Research Laboratories (KRL) uranium enrichment facility, returned home Friday morning, an associate of Chohan's family told AFP.
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.
Some reports quoted witnesses saying Caucasian men wearing bulletproof jackets took them from their homes, triggering accusations that United States intelligence agencies were involved.
Pakistani officials denied the pair were in custody, saying they were merely undergoing "personnel dependability and debriefing programs."
Earlier Friday a senior government official told AFP the two scientists were "neither arrested nor detained."
"They are undergoing debriefing sessions conducted by officials from within the sensitive organisations," said the official, who could not be named.
The term "sensitive organisations" is used in Pakistan to refer to intelligence agencies.
The government official said there were no specific charges against Muhammad and Chohan.
"This exercise does not stem from any specific charges against these individuals," he said.
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 AFP in a written response to e-mailed questions.
"People in debriefing sessions are not held in 'custody'."
Khan said the scientists had also been undergoing "personnel dependability" assessments.
But he declined to answer whether the men had freedom of movement.
Muhammad's daughter refused to comment on her father's whereabouts when contacted by AFP on Thursday, saying only that her family was fine.
Opposition parties are furious at the scientists' apparent detention and have accused President Pervez Musharraf of trying to appease the United States. The United States has said it would step up its effort to prevent nuclear technology reaching Iran, alleged by Washington to be using an atomic energy program as a cover to develop nuclear weapons.
Pakistan, which declared its nuclear capability in May 1998 with a series of underground nuclear tests, has been accused of sharing nuclear technology with both Iran and North Korea.
It adamantly denies any kind of nuclear proliferation.