His words, the strongest yet from the government, came as thousands of Indians - many calling for war with Pakistan - held a vigil in Mumbai to mark one week since the start of the rampage that killed 171 people.
While searching through about 150 bags, which police believed were left by the dozens of victims in the Chhatrapati Shivaji Terminus station, an officer found a suspicious-looking bag and called the bomb squad, said Assistant Commissioner of Police Bapu Domre. Inside were two 8.8-pound bombs, which were taken away and safely detonated, he said.
After the attacks, police found unexploded bombs at several of the sites, including two luxury hotels and a Jewish center.
It was not immediately clear why the bags at the station were not examined earlier. The station, which serves hundreds of thousands of commuters, was declared safe and reopened hours after the attack.
The discovery has added to increasing accusations that India's security forces missed warnings and bungled its response to the Nov. 26-29 attacks.
Indian navy chief Sureesh Mehta has called the response to the attacks "a systemic failure." The country's top law enforcement official has resigned and two top state officials have offered to quit amid criticism that the 10 gunmen appeared better trained, better coordinated and better armed than police in Mumbai.
Mukherjee on Wednesday adopted a more strident tone against longtime rival Pakistan.
"There is no doubt the terrorist attacks in Mumbai were perpetrated by individuals who came from Pakistan and whose controllers are in Pakistan," Mukherjee said after a meeting with Secretary of State Condoleezza Rice, visiting as part of a U.S. effort to ease tensions in the region.
"The government of India is determined to act decisively to protect Indian territorial integrity and the right of our citizens to a peaceful life, with all the means at our disposal," he said, a turnaround from earlier statements that ruled out military action.
Rice urged Pakistan to act "transparently, urgently and fully," saying Islamabad has a "special responsibility" to cooperate with the investigation. She noted that with six Americans killed in the attacks, the U.S. was cooperating closely with India.
Many Indians wanted more than just harsh words.
At the candlelight gathering in Mumbai, the mood was largely belligerent, with many calling for war.
"India should attack Pakistan right away," said Sandeep Ambili, 27, who works for a shipping company.
"Something has to be done. Pakistan has been attacking my country for a long time," said another protester, Rajat Sehgal. "If it means me going to war, I don't mind."
Others chanted anti-Pakistan slogans and held banners reading: "Enough is enough, go for war."
Similar rallies were held in cities across India.
Amid the cries for war, Indian Defense Minister A.K. Antony summoned the army, navy and air force chiefs to warn them to be prepared for terrorist attacks from the air and the sea in the wake of growing criticism about slack security.
Antony told the military chiefs they needed to improve intelligence coordination so that security forces can act on all credible threats, according to a statement.
It said Antony discussed increasing maritime security and "reviewed in detail the preparedness against any possible terror threats from air."
Defense Ministry spokesman Sitanshu Kar said the moves were a precaution and not based on concrete intelligence.
"We saw how they came through the sea routes," Kar said. "We are not ruling out any threats. It's a preventive measure."
Senior Bush administration officials and a foreign government official said Washington had advised India that a waterborne attack on Mumbai appeared to be in the works, and that Westerners and Israelis might be targeted. They spoke on condition of anonymity because of the sensitive nature of intelligence information. The officials would not elaborate on details of the U.S. warning. However, they said the warning information was too general for India to take immediate action.
Early Thursday, media reports said airports were put on high alert following intelligence warnings that terrorists were planning attacks on an airport in the next few days.
The Press Trust of India news agency, quoting unidentified sources, said "specific" information regarding planned attacks had been received. Phones at police headquarters and the New Delhi airport rang unanswered late Wednesday.
Analysts said the army had told the government that a large deployment of troops, like that which followed a 2001 attack on India's parliament, was not possible at present.
"The three services chiefs told the government four days ago that a full military deployment will not be a feasible option," said Rahul Bedi, a South Asia expert with the London-based Jane's Defense Weekly.
After the 2001 attack, India and Pakistan posted nearly 1 million soldiers along their border in a yearlong standoff.
Bedi said the army was reluctant to repeat that without a clear political objective spelled out by the government.
The two nations have fought three wars since independence from Britain in 1947, and neither government wants a fourth. Both now have nuclear weapons.
India fears the consequences of war on the huge economic gains it has made recently, while Pakistan has its own conflict with Islamic militants on the Afghan border.
Nevertheless, Mukherjee said India was now waiting for Pakistan. "What action will be taken by (the Indian) government will depend on the response that we have from the Pakistan authorities," he said.
India has called on Pakistan to turn over 20 people who are "fugitives of Indian law" and wanted for questioning, but Pakistani President Asif Ali Zardari said the suspects would be tried in Pakistan if there is evidence of wrongdoing.
"At the moment, these are just names of individuals - no proof and no investigation," he told CNN. "If we had the proof, we would try them in our courts and we would try them in our land and we would sentence them."
Much of the evidence that Pakistanis were behind the attack comes from the interrogation of the surviving gunman, who told police that he and the other nine attackers had trained for months in camps in Pakistan operated by the banned militant group Lashkar-e-Taiba.
Ajmal Amir Kasab, 21, told investigators his recruiters promised to pay his family from an impoverished village Pakistan's Punjab region $1,250 when he became a martyr.
Kasab said he and the other gunmen were "hand-picked" for the mission and trained for more than a year by Lashkar-e-Taiba, based in Kashmir, according to two senior officials involved in the investigation.
Kasab gave a detailed account of how he and another gunman roamed the train station and shot passengers, killed several police officers, and planted a bomb in a taxi, the officials said, speaking on condition of anonymity because they were not authorized to talk to media about the investigation.
Associated Press writers Erika Kinetz and Ravi Nessman in Mumbai and Ashok Sharma, Jeremiah Marquez and Anne Gearan in New Delhi contributed to this report.