The comments appeared to signal an abrupt shift in India-Pakistan relations, which had warmed in recent years, and came as Indian authorities named a third suspect in Tuesday's train bombings that killed 200 people and injured 700.
Prime Minister Manmohan Singh told a news conference that the bombers were "supported by elements across the border," a reference to Pakistan.
"If the acts of terrorism are not controlled it is exceedingly difficult for any government to carry forward what may be called the normalization and the peace process," he said.
In an immediate fallout, scheduled talks between the foreign secretaries of the two countries on July 20 appeared to have been scuttled. The talks were to review the progress of the third round of their dialogue process.
Press Trust of India news agency quoted "official sources," a euphemism for top government officials, as saying that there was little possibility of the talks taking place in the wake of the Bombay tragedy.
In Islamabad, Pakistani Foreign Ministry spokeswoman Tasnim Aslam said Singh's accusations were "unsubstantiated and we have already rejected them."
She said the peace process was in the interest of everybody in the region "and that is why we believe that the peace process must be continued and carried forward."
Earlier Friday, Bombay Police Commissioner A.N. Roy said a man known only as Rahil was the third person being sought in connection with the blasts. The photos of were released Thursday. The nationalities of the three men have not been given.
Investigators are casting a wide net in their hunt for the assailants, scrutinizing a Pakistan-based Islamic militant network, the Lashkar-e-Tayyaba, along with smaller homegrown groups.
An Indian Home Ministry official said that among the leads being followed by investigators was the possible involvement of the outlawed Students Islamic Movement of India, which may have been aided by Pakistan's Inter-Services Intelligence agency.