The Obama administration, in deciding to try alleged Sept. 11 conspirators in a New York courtroom, has said it is setting its sights on convictions, but some critics say a civilian trial -- instead of a military tribunal -- could end up targeting the Bush administration and its anti-terror policies.

One of those five defendants, Khalid Sheikh Mohammed, has been at the center of the debate over those Bush-era polices, in particular the harsh interrogation techniques used on Mohammed and others in an effort to obtain information on Al Qaeda and any additional attacks.

"The government is going to try to put Khalid Sheik Mohammed on trial. Defense lawyers will try and put the government on trial," former New York City Mayor Rudy Giuliani told Fox News.

The Justice Department says in a 2005 memo that CIA interrogators subjected Mohammed 183 times to waterboarding, a near-drowning technique described by Obama officials as illegal torture. But others disagree with Obama, most notably former Vice President Dick Cheney, who argues that the techniques used have kept the country safe from another attack.

Obama's attorney general, Eric Holder, announced in the summer that he would investigate whether CIA officers should be prosecuted for their interrogations, setting off intense debate over the prospect of prosecuting officials from the previous administration.

But on Friday, in announcing a civilian trial for Mohammed and four other detainees, Holder dismissed questions about whether politics was a factor in the decision.

"My job as attorney general is to look at the law, apply the facts to the law and ultimately do what I think is in the best interests of this country and our system of justice. Those are my guides," he said. "To the extent that there are political consequences, well, you know, I'll just have to take my lumps, to the extent that those are set in my way."

"But I think if people will, in a neutral and detached way, look at the decision that I have made today, understand the reasons why I made those decisions, and try to do something that's rare in Washington -- leave the politics out of it and focus on what's in the best interest of this country -- I think the criticism will be relatively mild."

But Holder already has faced strong criticism from conservatives and some families of 9/11 victims.

Karl Rove, a former top Bush adviser and now a Fox News contributor, said some attorneys in the Justice Department have tried for years to undermine the military tribunals system and "gain for these war criminals the rights that we would accord American citizens who might be accused of knocking over the local 7-Eleven."

"I think we make a mistake by focusing on the politics of it," Rove said. "What we ought to do is focus on the real danger this represents to the American interest and to the American security in the years ahead."

Supporters of trying the detainees in military tribunals note that the tribunals have relaxed standards for presenting evidence and offer minimized risk of disclosing government anti-terror secrets.

Tom Ridge, head of the Homeland Security Department in the Bush administration, warned against using the trials as a means of going after Bush administration officials.

"You'd like to think that ... it is simply their interpretation that these individuals are entitled to these kinds of criminal justice protections -- rather than using it as a fishing expedition to revisit decisions made during the past six years," he told FoxNews.com, adding that "time will tell."

"If we discover later that it's really just a facade to delve into a fishing expedition, I would find that just unacceptable, outrageous and a further distortion of the system," he said. "If it's subterfuge for the fishing expedition, that's just wrong and unconscionable."

FoxNews.com's Stephen Clark and Joseph Abrams contributed to this report.