A Honduran man seeking a safe haven in the United States said a Border Patrol officer told him that he would not be granted asylum — a determination the officer was not authorized to make — and when the migrant refused to sign paperwork, the officer said he would be sent to jail, where he would be raped.

In a report prepared by an asylum officer at Citizenship and Immigration Services, the officer wrote that threatening rape for refusing to sign paperwork was “a gross violation.”

“I’m really sorry that this happened to you,” the asylum officer recalled telling the man. “It should not have happened.”

In a separate account of misconduct, a migrant told an asylum officer that after she tried to run from a Border Patrol officer along the southwestern border in April 2017, “he caught me and threw me to the ground in a very aggressive way. And he pulled me up three or four times, and kept slamming me on the ground.” She said the officer also grabbed her by the hair and kicked her in the rib cage and lower pelvis, causing her to bleed.

These and other accounts are among 160 reports filed by federal asylum officers from 2016 to 2021, relaying details of abuse that asylum seekers described experiencing during interactions with border officials and while in U.S. custody. The descriptions, disclosed in response to a public records request made by Human Rights Watch, did not include information about the outcomes of the cases, including whether the complaints were found to have merit. And many other details, including dates and locations, were redacted.

While the complaints are mostly based on interactions that took place during the Trump administration, they come at a time of increased concern about the treatment of migrants by American border and immigration officials. Scenes last month of Border Patrol agents on horseback in Del Rio, Texas, corralling Black migrants with their reins have renewed a focus on years of complaints about inhumane treatment of undocumented immigrants.

“The department does not tolerate any form of abuse or misconduct,” a homeland security spokeswoman, Marsha Espinosa, said in a statement on Wednesday night. Ms. Espinosa said that under the leadership of its secretary, Alejandro N. Mayorkas, the department was conducting internal reviews “to identify and terminate intolerable prejudice and reform its policies and training,” and on the use of force. The agency has also added more personnel to its Office for Civil Rights and Civil Liberties, she said, and has issued memos on “the need to respect the dignity of every individual, fight against discrimination, and safeguard civil rights and civil liberties.”

President Biden has promised that the Border Patrol agents captured on camera in Del Rio would “pay” for their behavior. An internal investigation into their actions is underway, and Biden administration officials have promised to publicly share the findings. But in the past, there has been little transparency about such investigations, or disciplinary measures.

During his confirmation hearing on Tuesday, Mr. Biden’s choice to lead Customs and Border Protection, Chris Magnus, promised lawmakers that he would be forthcoming about the Del Rio investigation.

“I have a long history of transparency and sharing things with the public, whatever the outcome may be, because I think this is how you sustain and build trust,” said Mr. Magnus, the police chief in Tucson, Ariz. Mr. Magnus has a reputation for changing the culture of law enforcement organizations and said that after Del Rio, “examining tactics and training is certainly appropriate.”

When migrants are caught crossing the border illegally, a Border Patrol officer will detain and question them. Although the policy has changed temporarily during the pandemic, the officers are supposed to ask if the migrants fear persecution or harm in their home country. If migrants express a credible fear about returning, they are placed into immigration court proceedings and eventually interviewed by an asylum officer.

The records obtained by Human Rights Watch are of reports that asylum officers made after hearing allegations of law enforcement misconduct. In addition to complaints about physical, emotional and sexual abuse, migrants said in some of the reports that they were not asked whether they feared persecution; that they were told they could not request asylum; that they were pressured with threats to sign documents; and, in a few cases, that they had their documents torn up by border officers.

“The documents make clear that reports of grievous C.B.P. abuses — physical and sexual assaults, abusive detention conditions and violations of due process — are an open secret within D.H.S.,” said Clara Long, an associate director at Human Rights Watch, using the abbreviations for Customs and Border Protection and the Department of Homeland Security. “They paint a picture of D.H.S. as an agency that appears to have normalized shocking abuses at the U.S. border.”

The documents also show federal asylum officers apologizing for the treatment asylum seekers faced in U.S. custody. In March 2019, one asylum officer said to an immigrant: “U.S. government officials should not be treating you this way. They should be treating you and anyone else with respect.”

It is not clear how many interviews asylum officers conducted during the period that the more than 160 complaints were reported. According to immigration data, from 2016 to 2020, there were 409,000 referrals for credible fear interviews with asylum officers.

Similar complaints have been disclosed previously. In 2014, the American Immigration Council obtained records detailing more than 800 complaints against border officials, also through a public records request. In a subsequent request, the organization found that out of more than 2,000 allegations of misconduct by border officials filed from 2012 to 2015, more than 95 percent of the cases ended in no action against the accused.

Around 2013, some of the asylum officers working at Citizenship and Immigration Services reached out to a supervisor to see what could be done about the complaints they were hearing from migrants, a former asylum officer said. The former officer was not authorized to publicly discuss the internal workings of the agency and spoke on the condition of anonymity. The reports from migrants were troubling, the former officer said, and they wanted a formal system to document the complaints.

In 2015, the agency issued a directive to asylum officers to report known or suspected misconduct.

The allegations sought by Human Rights Watch had been sent to the Department of Homeland Security’s inspector general. The group asked the department last month about the outcomes of the complaints, but has not received a response, Ms. Long said.

In the reports filed by asylum officers, migrants described being called “pigs,” “herds of animals” and a “parasite.”

“They treat you like you are worthless, like you are not a human,” one asylum applicant said in September 2018.

Mr. Mayorkas said last month that the images from Del Rio “do not reflect who we are as a department, nor who we are as a country.”

But many immigrant advocates said rough treatment of migrants by Border Patrol agents was par for the course.

This argument was used in defense of a Border Patrol agent who admitted to deliberately running over a Guatemalan migrant, Antolin Rolando Lopez-Aguilar, in December 2017. A few weeks before the episode, the agent, Matthew Bowen, referred in text messages to immigrants as “mindless murdering savages,” “subhuman” and “unworthy of being kindling for a fire.”

In the court filings, Mr. Bowen’s lawyer argued that his client’s views were “commonplace throughout the Border Patrol’s Tucson sector.”

“It is part of the agency’s culture,” he said.