By Priscilla Alvarez and Geneva Sands | CNN

The Senate confirmed President Joe Biden’s pick to lead US Customs and Border Protection, Chris Magnus, on Tuesday after months of confirmation setbacks that left the agency with a void at the top amid a record number of border arrests.

The vote was 50-47, with Republican Sen. Susan Collins of Maine voting in favor of Magnus.

Magnus, who served as police chief in Tucson, Arizona, will inherit an agency of more than 60,000 employees, putting him in charge of the largest federal law enforcement agency and the second-largest revenue-collecting source in the federal government. Customs and Border Protection hasn’t had a Senate-confirmed leader since 2019.

“There is no doubt in my mind that Chief Magnus has the right qualifications for this position,” Democratic Sen. Ron Wyden of Oregon, chair of the Senate Finance Committee, said Tuesday on the Senate floor. “His range of experience in law enforcement all over the country makes him an ideal pick to lead an agency with tens of thousands of employees staffing more than 300 points of entry to the US.”

Before landing the job in Arizona, Magnus served as chief of the Richmond Police Department.

Magnus had a reputation for being a “strong community partner” while in Richmond, said Contra Costa County Supervisor John Gioia, who represents Richmond and other parts of the western county.

“Based on his record, he will bring a humane approach to border security,” Gioia said. “That’s who he is as a person and professionally.”

He added, “This is a high visibility, controversial job — it’s going to take someone who is strong in law enforcement but also humane and understands the complexities of these issues.”

Magnus gained national prominence in 2014 while chief of the Richmond Police Department after photos of him holding a Black Lives Matter sign at a Richmond protest against police violence went viral.

Magnus comes in at a time when Customs and Border Protection, which is under the Department of Homeland Security, has faced an influx of migrants crossing the US-Mexico border and grappled with travel restrictions stemming from the coronavirus pandemic.

A few months after Biden took office, Customs and Border Protection was overwhelmed by a surge of unaccompanied children arriving at the southern border. In September, thousands of migrants arrived at the Texas border town of Del Rio, where they gathered in squalid conditions under a bridge while awaiting processing in the US.

US Border Patrol, a division of Customs and Border Protection, made nearly 1.66 million arrests over the past fiscal year for unlawful crossings on the US-Mexico border, the highest annual number of apprehensions on record.

Magnus acknowledged the challenge before him during his nomination hearing in October, saying: “More than a few colleagues, friends and family members have asked me, ‘What are you thinking?’ Why would I choose to take on the important but challenging responsibility of leading CBP at this moment?”

“I want to make a difference,” he said.

As head of the agency, Magnus will be responsible, in part, for managing two controversial Trump-era border policies that have been kept in place or reimplemented under the Biden administration.

During his October hearing, Magnus voiced support for the public health order known as Title 42, which allows border officials to swiftly remove migrants encountered at the border, a policy launched by Trump administration in response to the pandemic. The policy has been criticized by immigrant advocates and Democratic lawmakers for largely barring migrants from seeking asylum at the US southern border.

“As a paramedic for 10 years public health has always been one of my top concerns, and because of that I think it’s absolutely imperative that we do everything possible to stop the spread of Covid. And Title 42 is a CDC authority, and I think it helps with this,” Magnus said during the hearing.

On Monday, the Biden administration relaunched the Trump-era border policy known as “Remain in Mexico,” restarting a program that allows officials to send non-Mexican migrants to Mexico to await their US immigration court hearings. Biden had pledged to end the program, but a federal judge in Texas ordered the administration to revive it.

Magnus’ nomination had initially been delayed by Wyden, who requested additional information from DHS about the Portland protests last year. Republican Sen. James Lankford of Oklahoma later put a hold on DHS nominations, including Magnus’, while seeking answers on immigration-related issues.

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Career official Troy Miller has led Customs and Border Protection in an acting capacity since Biden took office in January. Several top career officials at the agency who had served in the Trump administration either left or were forced out after Biden entered office, making the change in leadership even more notable.

Staff writer Annie Sciacca contributed to this report.