Relations between India and Pakistan have deteriorated since the attack, which India has blamed on the Pakistani group Lashkar-e-Taiba.
Pakistan, which has detained scores of members of Lashkar and an affiliated Islamic charity, the Jamaat-ud-Dawa, has been angered by Indian claims that Pakistani state agencies were involved and what it sees as repeated Indian hints of military action.
Mukherjee also told Al Jazeera that US hopes of combatting a growing Taliban insurgency in Afghanistan "cannot be de-linked" with Pakistan and that India considered Pakistan's co-operation and involvement "necessary" to resolve the crisis.
Barack Obama, the US president, has made Afghanistan the focus of his foreign policy and recently appointed veteran US diplomat Richard Holbrooke as the new envoy to Afghanistan and Pakistan.
The Indian foreign minister acknowledged that the Indian government had lobbied actively for India not to be included in Holbrooke's remit alongside the other two nations - particularly over its battle with Pakistan over the Kashmir region - but denied that this would affect India's relationship with Pakistan.
"In the last four years ... there has been substantial improvement [in relations with Pakistan]. We are talking of trade; we are talking of economic co-operation."
"India’s issue is not whether there will be any conflict between India and Pakistan. The issue is how to tackle the problem of terrorism ... emanating from Pakistan."
Mukherjee also said that any future talks on the status of Kashmir, which Obama has also pledged to broach with both India and Pakistan, would be postponed until Pakistan co-operated over the Mumbai attacks and took action against its perpetrators.
Tens of thousands of people have died in the Kashmir region, over which India and Pakistan have fought three wars and where there has also been a bloody battle against Indian rule in the territory since 1989.