The remarks by Pakistan's defense minister came hours after Indian Prime Minister Manmohan Singh said militants based outside his country carried them out.
Singh did not single out Pakistan, which New Delhi has accused of complicity in terror attacks on its soil before, but his remarks are likely to be taken as a sign here that India suspects Pakistani links somewhere in the plot.
A serious deterioration in relations between Pakistan and India, which have fought three wars since 1947, would greatly complicate U.S. foreign policy in South Asia as it tries to get Islamabad to focus less on its southern neighbor and more on tackling al Qaeda and Taliban militants along the Afghan border.
In 2001, militants fighting Indian-rule in the disputed Himalayan region of Kashmir attacked the parliament in New Delhi, helping push the countries to the brink of war a year later.
The attack late Wednesday saw teams of gunmen attack at least 10 sites, including two luxury hotels, a railway station and a Jewish center, in the financial capital of Mumbai. More than 100 people were killed.
In an address to the nation, Prime Minister Singh said the group that carried out the attacks "was based outside the country" and warned its neighbors "that the use of their territory for launching attacks on us will not be tolerated."
Pakistan Defense Minister Ahmed Mukhtar condemned the attack, but said "we should not be blamed like in the past,"
"This will destroy all the goodwill we created together after years of bitterness," he told The Associated Press. "I will say in very categoric terms that Pakistan is not involved in these gory incidents."
Earlier, Indian navy spokesman Capt. Manohar Nambiar said navy officers had boarded a cargo vessel it suspected of ties to the attacks that had come to Mumbai from Karachi, Pakistan. He later said the ship was not linked in any way to the strikes.
Many analysts said Wednesday's attacks were more likely to have been carried out by indigenous, Indian extremist groups blamed for a series of bombings this year than Pakistani-linked ones.
They also noted that India's government stood to benefit politically for hinting at the involvement of its old rival - rather than admitting some of its own 145 million Muslims had become radicalized.
"It will always want to label this militancy as foreign rather than to accept it has its own problem," said Shaun Gregory, an expert on South Asian terrorism at the University of Bradford in Britain. "That sells much more easily to the Indian public than admitting serious grievances within its Muslims."
Relations between India and Pakistan have improved in recent years, helped by a reduction in the flow of militants into Kashmir, the divided and violence-torn territory at the core of their dispute.
Pakistan's new president, Asif Ali Zardari, declared over the weekend that India posed no threat to Pakistan and called for the heavily militarized border to be opened for trade.
Earlier, Pakistan's foreign minister said his country would cooperate in any investigation. He too warned against early speculation about the perpetrators.
"Let us not go in for knee-jerk reactions," said Shah Mehmood Qureshi, who was in India for talks on a slow-moving South Asian peace process.
An Indian media report said a previously unknown group calling itself the Deccan Mujahideen claimed responsibility for the attacks in e-mails to several media outlets. There was no way to verify that claim.
Rohan Gunaratna, a terrorism expert at the International Center for Political Violence and Terrorism Research in Singapore, said he believed the terrorists were from India.
"The earlier generation of terrorist groups in India were mostly linked to Pakistan," he said. "But today we are seeing a dramatic change. They are almost all homegrown groups."