The Council on American-Islamic Relations said it received 1,019 claims of physical and verbal attacks on Muslims, on-the-job discrimination, and racial profiling by law enforcement.
In 2002, the organization received 602 such complaints.
The report cautioned that the jump partly reflected an increase in the number of regional offices opened by the Washington-based advocacy group, which allowed more cases to be documented.
The council blamed continued fear among Americans following the terrorist attacks of Sept. 11, 2001, and rhetoric that demeaned Islam and depicted Muslims as enemies of the United States during the war on Iraq.
It also blamed misapplication of the USA Patriot Act, the anti-terrorism bill that the Bush administration has defended as critical to national security. The civil liberties restrictions in the bill disproportionately hurt Muslims, the council said.
The full report will be presented at a news conference Monday at the National Press Club in Washington.
California saw the largest number of complaints, at 221, followed by New York at 191, Virginia at 69 and Texas at 57.
Reports of beatings and vandalism on Muslim-owned property more than roughly doubled to 93 last year. In Virginia, a Muslim woman who was wearing a veil was stabbed after being called a "terrorist."
While American Muslims continued to complain of harassment in airports, these claims dropped by about half, to 41. The decrease likely reflected a partial easing of the intense scrutiny of Muslims immediately after Sept. 11, the report said.
School complaints increased from 42 to 71, including several reports of anti-Muslim literature being distributed on campuses.
The organization wants Congress to hold hearings on post-Sept. 11 civil rights abuses and enact laws that would protect Muslims and others from harassment by police and employers.
In the most recent , released in November, there were 155 hate crime incidents listed as anti-Islamic in 2002, down sharply from the 481 reported in 2001.
In addition, there were 622 hate crime incidents listed in 2002 against ethnic groups that include people of Middle Eastern descent, down from 1,500 in 2001. There were 931 anti-Jewish incidents in 2002, slightly below the number in 2001.
Last year, a report by the Justice Department's inspector general that in the Bush administration's actions toward 762 foreigners held on immigration violations after Sept. 11.
The FBI took too long to determine whether they were involved with terrorism, as dozens endured "lock-down" conditions 23 hours each day and slept under bright lights, the report found.
Many if not most of the more than 700 detainees at issue in the case have since been deported. Some picked up after Sept. 11 were charged with crimes, and others were held as material witnesses. Only Zacarias Moussaoui, who was detained before the Sept. 11 attacks, is being prosecuted in connection with the Sept. 11 attacks.
A separate report last year found credible evidence that some detainees were beaten. The December 2003 report said there was evidence that some officers at the facility where detainees were held "slammed and bounced detainees into the walls … and inappropriately pressed detainees' heads against walls."
"We also found that some officers inappropriately twisted and bent detainees' arms, hands, wrists, and fingers, and caused them unnecessary physical pain; inappropriately carried or lifted detainees; and raised or pulled detainees' arms in painful ways," the report read. "In addition, we believe some officers improperly used handcuffs, occasionally stepped on compliant detainees' leg restraint chains, and were needlessly forceful and rough with the detainees."
The Supreme Court in January and other details about hundreds of foreigners detained in the months after the Sept. 11 terror attacks.
The high court turned down a request to review the secrecy surrounding detainees, nearly all Arabs or Muslims.
But two Middle Eastern immigrants have come forward to allege they were placed in solitary confinement, beaten and verbally abused at a federal lock-up.
Javaid Iqbal, a former cable technician, and Ehab Elmaghraby, a former restaurant worker, say they were shackled, shoved into walls, punched and called "terrorists" and epithets.
The men allege that federal agents apprehended them on suspicion of terrorist ties and held them for months at the Metropolitan Detention Center in Brooklyn.
They said they were kept in solitary confinement for 23 hours a day and denied adequate meals and medical care, The New York Times reported Monday. Iqbal, who was held for almost a year, said he lost 40 pounds in detention; Elmaghraby was held for nine months.
"I was in life and I went to hell," Elmaghraby told the Times.
The men were eventually cleared of terrorist ties but were deported to their homelands after pleading guilty to minor federal criminal charges.