The pardon granted to metallurgist Abdul Qadeer Khan relates only to his admission that he transferred nuclear technology to Iran, North Korea and Libya, Pakistan said on Monday.
"The pardon is specific to the charges made so far, and about which Dr A Q Khan has made a confessional statement... this is not a blanket pardon," foreign office spokesman Masood Khan said in Islamabad.
Asked if Khan could be prosecuted in future, he said, "The investigations are continuing and they have not come to a closure."
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He said there are strict security restrictions imposed on Khan and other tainted scientists. "Khan and those who have been investigated will not be allowed to resume their duties or activities. This has to understood clearly."
He said Khan "has been cooperating with our authorities. We expect he will continue to cooperate."
Asked how he could redefine the conditions of the pardon granted by President Pervez Musharraf, Khan said, "This is an authorised statement I made."
Two days ago, defence ministry spokesman Major General Shoukat Sultan had said the first information report against Khan was "sealed", meaning the case was closed as a result of the pardon.
The clarification comes in the wake of international concerns over the way Khan was let off.
