"I think they are taking liberties and they are taking short cuts - I was appalled."

This was the reaction of Jim Weddick, a retired FBI agent of 35 years, reviewing an FBI case against a suspected al-Qaeda cell in Lodi, California.

As defence consultant for Pakistani Americans Umer and Hamid Hyed, who were accused in 2005 of attending Pakistani terror training camps, Weddick's first job was to examine tapes of the FBI interrogations.

The case involving the father and son hinged on a contested confession, which was videotaped during a lengthy FBI interrogation.

"I was shocked, the agents seemed to be just leading Hamid Hyed and his father - there wasn't anything that I saw that suggested they were guilty," said Mr Weddick, who was not allowed to give evidence by the trial judge.

The jury were convinced, however, and Hamid Hyed was found guilty of aiding terrorists. An appeal is still pending.

Umer Hayat negotiated a plea bargain for a non-terrorist-related financial irregularity and was freed in return for time served while waiting for trial.

The event failed dramatically to find an active al-Qaeda cell in California.

Post 9/11 changes

In the course of producing The FBI at 100 for BBC Radio 4, presenter Tom Mangold and I have interviewed many past and serving agents like Mr Weddick who say they have seen their beloved Bureau undergo a huge change since 11 September 2001.

Hyed's case failed to find an active al-Qaeda cell in California

The USA Patriot Act, which was passed the following month, now allows the FBI to investigate suspects without first establishing a link to criminal activity; it can detain them for longer; and its powers of surveillance have been extended.

But Mr Weddick's worries about the possible temptation to short cut on justice are not shared by Philip Mudd, second-in-command at the FBI's National Security Branch.

"The new FBI represents an evolution," he says. "Our responsibility is not only to be the world's best investigators, but also to provide security for this country - by the use of the collection of intelligence and then the use of law-enforcement tools to pre-empt an operation before it happens."

Defending America's homeland against international threats is nothing new for the FBI, and the taking of liberties and the balance between national security and civil rights have been concerns since the first 34 agents were recruited in 1908 to investigative new crimes that crossed state borders.

In 1919, as America worried over colossal immigration from Europe, and the perceived threat of world Bolshevism, the Bureau of Investigation - as it was originally known - reacted to a series of terrorist attacks on the homes of American public figures by rounding up thousands of suspected communists and anarchists, and throwing them in jail for little more than their political beliefs.

Hoover's FBI

The raids were masterminded by a young lawyer in the Justice Department by the name of J Edgar Hoover.

After Hoover's death the FBI was stripped of many of its powers

Five years later, Mr Hoover was appointed director of the Bureau. He stayed for 48 years under eight presidents, all of whom were unable to replace him because of the mass of secret information he acquired on political enemies, friends, real and imagined enemies of the state, civil rights leaders, film stars, and any ordinary American who fell within earshot or phone tap of his 'G men'.

After his death in 1972, Congress stripped the FBI of many of its powers in reaction to revelations about Mr Hoover's excesses, including his Counter Intelligence Programme (Cointelpro), which at the time was seen by many as little more than a department of dirty tricks involving illegal or improper acts to harass and disrupt targets.

Buck Revell was an FBI man at the time.

"Probably not more than 200 agents in the whole organisation were involved in Cointelpro but all 9,000 agents at the time suffered embarrassment and loss of morale," he says.

"It was very embarrassing to an organisation charged with the responsibility of enforcing civil rights, to be found to be violating civil rights under these circumstances."

It is the Congressional firewall erected in the 1970s that many former agents like Mr Revell blame for the FBI's failure to predict or prevent the 9/11 attacks.

We've been told by the director repeatedly that we will become a national security bureau

Philip Mudd, FBI

Now the heavy pendulum of the Patriot Act has swung power back their way.

So is this a return to the bad old days? Not for Mr Mudd.

"People who look at the Hoover period and worry that we are going down the road towards abusing civil liberties, I believe are mistaken," he says.

"We've been told by the director repeatedly that we will become a national security bureau, we've been told by the American people this is what they expect, we've been told by presidential and Congressional commissions that we need to improve in this regard."

But in one sense, the Bureau has turned full circle. As it prepares for its second century, it is again focusing on new cross-border crimes. It's just that this time, the fight is borderless.

The FBI at 100 is being broadcast on Radio 4 this week and next week at 1545 GMT