India says it has handed over evidence linking Mumbai attacks to Pakistani "elements".
"What happened in Mumbai was an unpardonable crime," Mukherjee said.
"As far as the government of Pakistan is concerned, we ask only that it implement the bilateral commitments that it has made at the highest levels to India, and practises her international obligations."
India has blamed the Mumbai attacks on what it says are Pakistan-based groups, but Pakistan has denied the accusations saying it was yet to get proof.
"It is our expectation that the government of Pakistan will promptly undertake further investigations in Pakistan and share the results with us so as to bring the perpetrators to justice"
The attacks on multiple targets in India's financial capital lasted for nearly three days and left 179 people dead with hundreds more wounded.
"This material is linked to elements in Pakistan," an Indian government statement said, referring to the evidence handed over on Monday.
"It is our expectation that the government of Pakistan will promptly undertake further investigations in Pakistan and share the results with us so as to bring the perpetrators to justice."
Tensions between the nuclear-armed rivals have been high in the wake of the attacks, with Pakistan redeploying troops away from the Afghan border towards India.
The two countries have fought three wars against each other since they gained independence from Britain and partioned in 1947.
India has, however, been careful not to blame the attacks on the Pakistani government, and Monday's statement again accused "elements in Pakistan" of being behind the plot.
Much of the Indian evidence in the attacks comes from interrogations of Mohammed Ajmal Kasab, the only one of 10 attackers to survive.
Kasab has reportedly told Indian authorities that he and nine others were Pakistani nationals, that he was trained in Pakistan, and that his handlers are still there.
Pakistan has said it has no record of Kasab as a Pakistani citizen.