Mukherjee also said on Tuesday that it was not considering military action in response to the latest attacks in Mumbai that killed at least 177 people.
"Nobody is talking of military action," Mukherjee told reporters when asked about options on what action could be taken.
Mukherjee said that peace talks with Pakistan, a process which start in 2004, would be difficult to continue after the attacks.
"We have no intention of not carrying out the peace process," he told Indian news channel NDTV.
"If these incidents ... are not adequately addressed by [Pakistan], it becomes difficult to carry out business as usual and that includes the peace process."
Indian investigators have said the attacks were carried out by the Lashkar-e-Taiba, a group based in Pakistan.
A senior US state department official said on Tuesday that a group based in Pakistan may have been responsible for the attacks.
"There are a lot of reasons to think it might be a group, partially or wholly a group, that is located on Pakistan's territory," the official, who declined to be named, said at a meeting of Nato foreign ministers in Brussels.
Condoleezza Rice, the US secretary of state, urged Pakistan to give its "absolute, total" co-operation in finding those responsible for last week's attacks.
Rice, who is due in India on Wednesday for talks aimed at easing tensions between India and Pakistan, said the US had made clear to Asif Ali Zardari, Pakistan's president, that there must be complete transparency in the investigation into the Mumbai attacks.
On Monday, a US official said the Bush administration had warned the Indian authorities of the possibility of a waterborne attack on Mumbai.
The official would not elaborate on the timing or details of the US warning.
India has formally accused what it called "elements" in Pakistan of being behind the group that staged the attacks across Mumbai.
"The high commissioner of Pakistan was called to the ministry of external affairs this evening. He was informed that the recent terrorist attack on Mumbai was carried out by elements from Pakistan," a Foreign ministry statement said.
The ministry said investigations had shown that all gunmen involved in the Mumbai attacks were Pakistani nationals.
New Delhi also demanded that Islamabad take "strong action" against those responsible.
Pakistan immediately hit back, with its foreign secretary summoning the Indian high commissioner in Islamabad to give a response to New Delhi's protest, the Press Trust of India has reported.
Pakistan's government denies it was in any way linked to the attacks on India's financial capital.
Al Jazeera's Kamal Hyder said the latest demand from India will put strains on relations between the two nuclear armed countries.
"The biggest problem is how people in Pakistan are saying that they cannot let the Indian government or the public win their anger against the country, which may or may not be responsible. They were sympathetic to the victims who suffered from the attacks, but now that feeling has been lost because of finger pointing.
"There is also a realisation that confrontation will not do the people of Pakistan or India any good.
"Dangerous times indeed, and there has to be international intervention to ease the tension."