"There was no consultation, no consultation with the police department. That decision was made. We were informed," Kelly said Tuesday.
When asked if the NYPD should have been asked about security and other considerations in advance of sending the accused terrorist to the scene of the attack, Kelly said," The fact is we weren't asked. And we will make the best of a situation. We weren't."
A spokesman for Mayor Bloomberg said the Mayor was only informed the morning Attorney General Eric Holder made his announcement.
Kelly said there are no new terror threats to New York City. But he added that moving "the trial here will do nothing to diminish that threat level."
Attorney General Holder announced his decision on November 13 to hold the 9-11 trial in federal court in Manhattan. The courthouse is located just blocks from 'Ground Zero.'
Holder has said he did not even consult the President before making his decision, but told the President the night before he went public with his decision.
Reaction to the controversial decision has been mixed. Some victims cheered the decision as a victory for the rule of law. Others argued the accused terrorists do not deserve their day in civilian court and that a military tribunal is more appropriate and secure.
Holder has said he consulted with Justice Department prosecutors and the Defense Department. He also told PBS that he consulted his brother, a retired Port Authority police officer who lost numerous friends in the 9-11 attacks.
Immediately after Holder's decision, the NYPD did issue a statement saying "It's highly appropriate that those accused in the deaths of nearly 3,000 human beings in New York City be tried here, and the NYPD is prepared for the security required."
A Justice Department spokesman Tuesday said, "The Department appreciates the strong support and cooperation we have already received from Mayor Bloomberg and Police Commissioner Kelly and we agree with them that we can safely hold these trials in Manhattan."
Khalid Shiekh Mohammed is the self-described mastermind of the 9-11 attacks. Nearly 3,000 people were killed in the attacks on the World Trade Center, the Pentagon and in a field in Pennsylvania.
The terror suspects are expected to arrive in New York early next year, at least 45 days after the Justice Department formally notifies Congress of its plans to bring the suspects here.
Holder's decision to put the al Qaeda suspects on trial in New York amid the Obama administration's efforts to close Guantanamo Bay.