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Patil riled citizens last week when he described the attack as a "minor incident" in an on-camera statement to reporters, saying that his government deserved credit for preventing further loss of life.
It's not yet known who will replace the two men, but news of their resignations came as little surprise after a week that has left Mumbai's residents shaken and furious with the men who attacked the city and with those who allowed it to happen, despite warnings from foreign nations, including the United States.
American intelligence officials told ABC News today that they warned Pakistan of a possible terror attack, even naming the Taj Mahl, scene of some of the bloodiest attacks, as a possible target.
Praveen Swamy, an analyst interviewed by ABC News, described the situation as "not an intelligence failure but a failure of intelligence."
That failure has been apparent in the days following the attack, as the politicians running the city seem to have utterly misjudged the public mood and the gravity of the assault, some say.
For example, critics charge that on the eve of his resignation, Deputy Minister Deshmukh turned his Sunday night visit to the ravaged Taj hotel into a Bollywood spectacle.
In full sight of television cameras, Deshmukh entered the lobby of the Taj accompanied by his son, Bollywood star Ritesh Deshmukh and Bollywood filmmaker Ram Gopal Varma, who is reportedly looking to make a film about the attacks.
Although Deshmukh later denied that he had arranged to escort Varma to the building, no private citizens are being allowed into any of the hotels, a fact that left many people wondering about the Bollywood director's presence there.
As the cleanup operation at the Taj hotel ended, with police retrieving bodies and searching for booby traps, tensions between India and Pakistan continued to rise.
U.S. Secretary of State Condoleezza Rice is expected to arrive in New Delhi, the Indian capital, Wednesday amid fears that the two nuclear-armed nations would increase their troop presence along the border.