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STANFORD — A delicate balance must be struck to protect the United States from another terrorist attack without violating the civil rights of Muslims here, FBI Director Robert Mueller said Friday. 

Speaking at Stanford University, Mueller said that as head of the nation’s lead agency handling counterterrorism he is wrestling with dilemmas finding that balance. 

“The overwhelming majority of Muslims in this country and around the world are peaceful, law-abiding citizens. A small number of Muslims, however, are members of radical fundamentalist sects sworn to the destruction of the United States,” he said. “This presents a dilemma for those charged with protecting against the next attack, raising difficult investigative issues for which there often is no clear answer.” 

Jean Hardisty, president of Somerville, Mass.-based Political Research Associates who has been studying post-9-11 policies, said Friday the Bush administration is failing to find balance between security and freedom for all Americans. 

“In my position as a middle-class, white, professional woman I don’t think my rights have been substantially impacted,” she said, “but for people who are more marginalized in society, for example immigrants of any status, are in a much more precarious position about having their freedom protected and their civil liberties protected,” she said. 

Since the terror attacks, there have been a series of federal actions, laws and new regulations that have drawn criticism from some civil rights activists. 

Federal authorities have detained more than 1,000 unidentified terrorism suspects, many of them for months. Agents have also listened in on conversations between detainees and their lawyers, questioned thousands of young Middle Eastern men who recently entered the country and tried noncitizens accused of terrorism in secret military tribunals. 

The U.S.A. Patriot Act approved a year ago included a wider use of roving wiretaps and the ability to subpoena email records provisions. 

And in May 2002, the Justice Department announced guidelines letting FBI agents investigating terrorism to monitor public gatherings, more closely scrutinize Internet usage, and send undercover agents into houses of worship without having clear prior evidence of possible criminal activity. 

The new guidelines set aside restrictions adopted in 1976 intended to curb practices associated with the FBI under former Director J. Edgar Hoover, including infiltrating left-wing groups and harassing such civil rights leaders as Martin Luther King, Jr. 

This week in Washington D.C. the American Civil Liberties Union launched a public advertising and lobbying campaign to press policy makers to revise some of the laws and policies passed after the terror attacks that they say do damage to civil rights. 

“We will work tirelessly so that our safety can be guaranteed simultaneously with our right to say what we want, befriend whoever we want, worship however we want and be who we are without fear that our lawful actions will land us on the governments radar screen,” said Laura Murphy, director of the ACLU’s Washington legislative office. 

Murphy said the Justice Department needs to reverse some of its new, more lenient guidelines. 

The ACLU also is pushing for judicial review before wiretapping, and says there should be no indefinite detention for non-citizens who are not dangerous. In addition, the ACLU said that dissident groups engaging in lawful activities — such as Operation Rescue, Greenpeace and PETA — should not be swept up in an overbroad definition of domestic terrorism. 

“Now more than ever, it is necessary to stand up for the Bill of Rights. We strongly believe that it is patriotic to question the actions of an overreaching government — one that seems determined to eliminate crucial checks and balances on its authority,” said Murphy. 

Mueller said he believes the United States needs to be careful not to be “too aggressive” and he agrees this is not the first time in U.S. history that conflicts have led to restricts on civil rights. 

“As you know, our nation does not have an unblemished record protecting Constitutional freedoms during times of crisis,” he said. 

Woodrow Wilson’s Espionage Act during World War I, upheld by the Supreme Court, banned statements that might interfere with military operations. And in World War II, more than 100,000 Japanese and Japanese-Americans were sent to internment camps. 

Mueller said he knows he will be judged by history, “not just on how we disrupt and deter terrorism, but also on how we protect the civil liberties and Constitutional rights of all Americans, including those Americans who wish us ill,” he said.