India on Wednesday turned down Pakistan's request for a joint investigation into the Samjhauta Express blasts case, but promised to share information on the probe.
After the Joint Commission meeting, the two neighbours also took a major step towards confidence building by signing an agreement on reducing the risk from accidents related to nuclear weapons.
"As per the law of the land, investigation is being carried out by India. We will carry on this investigation. Perpetrators of this heinous crime will be brought to book," Mukherjee said at a joint press conference with his Pakistan counterpart Khurshid Mehmood Kasuri.
Pakistan National Assembly had on Tuesday passed a resolution calling for a joint probe into the blasts in the Lahore-bound train near Panipat killing 68 persons, mostly Pakistanis.
Mukherjee said the joint anti-terror mechanism will meet in Islamabad on March 6 and it was the appropriate forum for sharing and acting on such information.
India, he said, was determined to bring to book perpetrators of the "heinous crime."
The terror attack figured prominently at the two-hour meeting of the Joint Commission co-chaired by Mukherjee and Kasuri.
Kasuri described the attack on the Samjhauta Express as a "horrendous tragedy" and an "act of heinous crime", which "underlines the need for cooperation" between the two countries in fighting terrorism.