Sen. Susan Collins said Tuesday she was most “surprised” and “troubled” by accounts found in the recent Sept. 11 commission’s report that revealed contradictory directives to military pilots about when to shoot down commercial airplanes.

She said formation of a new counter-terrorism agency should help clear up such confusion.

Collins was tapped last week to head up the Senate committee charged with crafting a bill aimed at implementing the commission’s major recommendations, including creation of a National Counter-terrorism Center and national intelligence director.

Hearings are set to start Friday with testimony by Sept. 11 commission Co-chairmen Tom Kane and Lee Hamilton. The hearings are expected to conclude in September, with draft legislation due by October, Collins said.

“That’s a very aggressive schedule and it’s going to require a lot of hard work during what is usually the August recess period,” she said.

Collins, who is back in Maine this week, said she plans to seek the testimony of most of the various 15 intelligence agencies’ directors, including three past Central Intelligence Agency directors.

John McLaughlin, acting CIA director, has panned the idea of creating a new agency and intelligence czar.

Collins said she expects there will be resistance from him and his peers.

“I think it’s predictable that the current agency heads will not be enthusiastic about these two recommendations,” she said. “Turf battles abound in Washington. Undertaking massive reorganizations requires a sea change in thinking and it requires determination and persistence.”

She said she is “convinced the recommendations are sound and should be pursued.”

Even before she was named to the job, Collins supported publicly the formation of a new anti-terrorism intelligence agency and director.

It is not a question of if they should be implemented, she said, but how.

“I don’t underestimate the difficulty of the task. There is going to be intransigence. There are people in the Senate who believe that this is not the right direction to go and obviously I’ve yet to meet an agency head who is eager to lose authority or jurisdiction.”

Other recommendations outlined by the Sept. 11 commission, dealing with border security and immigration, for example, will be taken up by her committee, likely after October, she said.

Collins said she has read much of the commission’s report already and plans to finish by Friday.

She said she also was surprised to learn about failures within both the Bush and Clinton administrations to “connect the dots” of signs and clues leading up to Sept. 11, 2001.

She cited the example of Osama bin Laden’s public appeal during a CNN interview in 1998 that it was every Muslim’s duty to kill as many Americans anywhere in the world as possible.

“I was surprised to read how blatant some of the miscues were,” she said.