This is the second time in less than a week that India has taken up the issue with Pakistan.
Earlier this week, foreign secretary Ranjan Mathai made the same appeal before his Pakistan counterpart Jalil Jilani in the delegation level talks in Delhi.
In his meeting with Khar in Tokyo, on the sidelines of the Tokyo Conference on Afghanistan, Krishna also thanked Pakistan for releasing another Indian prisoner Surjeet Singh who had served his sentence.
Krishna also discussed with Khar the disclosures made by Mumbai attacks accused Abu Jundal about the involvement of state actors in the November 2008 terror strike asking her to expedite the ongoing trial of some of the accused in Pakistan.
The pending visa agreement to facilitate trade between the two countries was also taken up.