An unauthorized immigrant complained that a Border Patrol agent hit his head against a rock, causing a hematoma.

A minor said an agent physically forced him to sign a document.

Another border crosser complained agents denied him water and touched female immigrants inappropriately.

Those were among the 279 complaints filed in the Border Patrol’s Tucson Sector between January 2009 and January 2012.

Only the first resulted in counseling for the agent — one of 13 complaints where a disciplinary action was taken out of 809 cases reviewed by the American Immigration Council, a D.C.–based immigrant advocacy group.

Many complaints were pending, but among the cases in which a formal decision was made, 97 percent resulted in “no action taken,” the researchers found.

Through a Freedom of Information Request, the group reviewed complaints filed against Border Patrol agents and supervisors from the three-year period.

Since there is no unified system through which the agency receives complaints, the report provides only a snapshot of those that were passed along to Customs and Border Protection’s office of internal affairs.

The agency released this statement Tuesday: “CBP is committed to ensuring that the agency is able to execute its challenging missions while preserving the human rights and dignity of those with whom we come in contact.

“The men and women of CBP strive to treat each of the over 1 million people we come into contact with each day with the respect they deserve. All allegations of misconduct are taken seriously, and if warranted, referred for appropriate investigative and/or disciplinary action to be taken.”

Mike Nicley, retired chief of the Border Patrol’s Tucson Sector, said the agency had issues with the level of experience in the past when it went through a hiring surge, and agents make mistakes. But overall, the number of complaints filed are a small percentage of total apprehensions and many are not substantiated.

It might be that the agent’s action is justified, he said, but the person involved doesn’t see it that way.

More than one in three complaints filed against Border Patrol were directed at agents in the Tucson Sector — the highest among the nine Southwest border sectors. But when apprehensions were taken into account, Tucson fell to sixth place, with 69.5 complaints filed per 100,000 apprehensions.

During the time of the review, Tucson still had the highest number of apprehensions, with more than 200,000 in fiscal years 2009 and 2010. Since, the number has dropped to about 120,000 and Tucson was surpassed last fiscal year by the Rio Grande Valley Sector in Texas, which recorded 154,453 apprehensions.

Researchers are just scratching the surface of how complex the system is, said Daniel Martinez, co-author and assistant professor of sociology at The George Washington University and head of the binational migrant border-crossing study.

He said many people don’t file formal complaints, especially if they get deported or are afraid due to their legal status.

Among the complaints reviewed, 40 percent were still “pending investigation.” As of January 2012, one case reviewed had been pending more than two years.

Seventy-eight percent of the cases filed were allegations of physical abuse, or excessive force, the data show. A much smaller number pertained to improper searches or inappropriate touching.

CBP, the parent agency of the Border Patrol, has been under increasing scrutiny from Congress, nonprofits and community members for what they consider a lack of accountability and transparency.

With more than 4,000 agents, the Border Patrol is one of the largest employers in the region.

“The buildup has not been matched with adequate accountability,” said Vicki Gaubeca, director of the American Civil Liberties Union’s regional center for border rights in New Mexico, during a conference call with reporters Tuesday.

Just last week, Mario Alvarado, a Pima County resident and U.S. citizen, filed a lawsuit against a group of Border Patrol agents for what he considered wrongful stops and abuse on multiple occasions during the summer and fall of 2012.

He was stopped and referred to secondary inspection at the I-19 checkpoint several times . On at least two occasions, he was detained for eight hours, court documents show.

During one of those stops, an agent accused him of being an illegal immigrant, buying his citizenship and being in possession of drugs.

Immigration and Customs Enforcement agents also arrested him in September at the port of entry after a code alerted them that Alvarado was armed and dangerous. When the agent looked at the computer system again, it showed a different code. He was released an hour later.

Border Patrol never charged Alvarado as a result of any of the multiple detentions, the lawsuit said.

Over the last several years, local nonprofits, including No More Deaths, and researchers with the University of Arizona have published reports that point to physical and verbal abuse of immigrants while in Border Patrol custody.

In March, an alliance of immigration advocacy groups launched the website to catalog lawsuits and administrative complaints brought against the agency.

The ACLU in Arizona recently filed a lawsuit to get records regarding Border Patrol checkpoints amid allegations of civil rights violations and unlawful stops.

Representatives of the ACLU and the Women’s Refugee Commission, which in 2012 published a report on unaccompanied children crossing the border, said during the conference call they have filed administrative complaints regarding CBP since 2012 and still have not gotten a response.

“We need a more effective, meaningful complaint system,” said Gaubeca, of the ACLU. “There’s no one way to file a complaint. And when we do file a complaint, there’s no adequate response.”

A bill introduced in March aims to do just that.

Rep. Beto O’Rourke, a Democrat from El Paso, and Steve Pearce, a Republican from New Mexico, introduced legislation that would create a new complaint system for CBP and an independent oversight commission.

“When the results of an investigation are not released timely or the public perceives there’s not transparency, that does more damage to the standing of the agency,” Nicley said.

Often it’s not up to the Border Patrol to release the information, he said. “The Border Patrol suffers when information is not made available.”