Yasin Chohan, a laboratory director at the Kahuta Research Laboratories (KRL) uranium enrichment facility, and KRL director Farooq Mohammad were taken from their homes in early December and held for questioning, opposition politicians and local media said.
Chohan returned home Friday morning, an associate of his family told AFP while Farooq's whereabouts were unknown.
"Farooq is still undergoing debriefing sessions," a senior security official told AFP.
Local newspapers had linked the pair's apparent detention to allegations that Pakistani scientists helped Iran develop its nuclear programs.
Pakistani officials have denied the pair were in custody, saying they were merely undergoing "routine 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" refers to intelligence agencies.
"This exercise does not stem from any specific charges against these individuals," he said.