MUMBAI, India  Indian commandos took control of the Taj Mahal Palace & Tower, the last nest of terrorist resistance, on Saturday morning, after a lengthy assault that left three terrorists dead and sections of the hotel in flames, the head of the commando unit said in a televised news conference.

Soldiers were still combing the hotel, going room to room in search of remaining gunmen, but the siege appeared finally to have ended, J. K. Dutt, director general of the National Security Guard, an elite commando force, said in the news conference at 9 a.m. Firefighters were permitted to begin pouring water over the flames that had burned out of control in the hotel’s lower floors for as much as an hour while the commandos battled the terrorists.

Image An Indian commando loaded his gun on Friday before an attack on militants holed up in a Jewish center in Mumbai. Commandos slid down ropes from a helicopter, and stormed the building. Credit... Michael Rubenstein for The New York Times

It was the third day of a siege that has shaken India, raised tensions with neighboring Pakistan and prompted questions about the failure of the authorities to anticipate the tragedy or to react swiftly enough as it unfolded.

All told, after attackers were cleared from a second hotel and a Jewish center on Friday, more than 150 people had died. Most of the dead were apparently Indian citizens, but at least 22 foreigners were killed. Among the dead reported were a rabbi from Brooklyn and his wife, who ran the Jewish center.

The main success for the authorities on Friday came at the second hotel, the Oberoi. The authorities said that two gunmen had been killed and 93 foreigners  some of them wearing Air France and Lufthansa uniforms  had been rescued, though 30 bodies were found. Survivors offered harrowing accounts of their ordeal, trapped on the upper floors of the high-rise hotel while gunmen prowled below. The National Security Guard said it recovered two AK-47s, a 9-millimeter pistol and some grenades.

Image A crowd in Mumbai gathered at a barricade down the street from Nariman House, the Jewish center. The dead included the centers rabbi, who held dual American and Israeli citizenship. Credit... Michael Rubenstein for The New York Times

For the first time, after several veiled accusations that Pakistan was involved, Indian officials specifically linked the attacks to their neighbor and longtime nemesis. India’s foreign minister blamed “elements in Pakistan” for the attacks , spreading the repercussions of the attacks beyond India’s borders. American intelligence and counterterrorism officials said Friday that there was mounting evidence that a Pakistani militant group  Lashkar-e-Taiba, which has long been involved in the conflict with India over the disputed territory of Kashmir  was responsible.

The Indian authorities were beginning to face sharp questions about why operations to flush out a handful of assailants at the Jewish center and at the Taj Mahal Palace & Tower had not moved more rapidly. And many other basic questions remained for a crisis that unfolded so publicly, on televisions, Web sites and Twitter feeds across the world. Who were the attackers? The police tally was at least 11 killed and one captured alive, but could so few militants have caused such mayhem?

Indian commandos said the attackers at the hotels were well trained, with one carrying a backpack packed with hundreds of rounds of ammunition, and they seemed to know the buildings’ layout better than the security forces, indicating a high degree of preparation. Some were seen arriving by boat; others may have been guests at the hotels for days.