A warrant for the arrest of San Francisco 49ers linebacker Ahmad Brooks on charges he assaulted a teammate has been put on hold amid a debate in the Santa Clara County District Attorney’s Office over whether Brooks should be charged with a felony or a misdemeanor — or not at all.

The controversy stems from a June 8 incident in which Brooks allegedly struck 49ers nose tackle Lamar Divens three times in the head with a beer bottle and then punched him in the face during an argument over car keys outside Brooks’ house in San Jose. The alleged attack left Divens bloodied and requiring three stitches, according to court documents.

At the time, Divens said he wanted to press charges, but he has since changed his mind, according to the warrant application. The alleged attack was also witnessed by two other unidentified team members, one of whom gave a recorded statement to police.

The decision by District Attorney Jeff Rosen over whether to pursue the case as line prosecutors desire could have a major impact on Brooks’ career and team, which is set to move to Santa Clara next year. Brooks, now 29, signed a six-year contract extension last year worth $44.5 million, with $17.5 million guaranteed. This season, he helped clinch the NFC Championship by knocking down a key third-down pass to thwart an Atlanta Falcons’ drive in the 49ers’ 28-24 win Jan. 20.

Rosen declined to comment. Brooks could not be reached for comment. The 49ers declined to comment.

In 2008, when Brooks was playing for the Cincinnati Bengals, he was accused of punching a woman in the face and accepted mediation on the charges, according to media reports. Brooks is 6-feet-4 and weighs about 260 pounds.

Also, at the end of the 2005 season, he was dismissed from the University of Virginia football team because of an unspecified “off the field” incident, according to the university. In 2003, he was charged with misdemeanor marijuana possession. Those charges were dismissed after he completed the requirements of his probation.

Buoyed by the taped eyewitness statement — and by Brooks’ prior record — prosecutors who routinely handle battery and assault cases submitted an application Thursday to Judge Sharon Chatman seeking an arrest warrant on a felony assault with great bodily injury charge. It carries a maximum sentence of four years behind bars.

A day later, after the judge signed the warrant, higher ranking officials in the DA’s office took the rare step of intervening and notified the court at 4:30 p.m. Friday to hold it, a court spokesman said. Sources said some members of Rosen’s administration view the case as a wobbler — meaning it could be pursued as a misdemeanor instead of a felony — and others want to drop it entirely.

The hesitation is unusual. The Santa Clara County DA’s office is widely known in the Bay Area for being the toughest of all nine area offices on crime.

According to the application for Brooks’ arrest, the incident unfolded after Brooks, Divens and other 49er players spent the evening of June 7 at different players’ houses. Eventually they decided to go to downtown San Jose and keep drinking.

The unidentified witness said Brooks was too intoxicated to drive home, so Divens drove. When they got to Brooks’ house about 2 a.m. on June 8, Brooks asked for his keys. Divens pretended to chuck them onto the grass and then started to hand them to him.

Brooks then allegedly clocked Divens in the head with a beer bottle. Brooks allegedly began cursing and then struck him in the head again. Brooks allegedly asked Divens, “Do I need to get my (expletive deleted) gun?” and struck him again. Prosecutors also allege in the warrant that Brooks punched Divens.

Police took a report but did not make any arrests. According to the court documents, a San Jose police sergeant called Divens three days after the incident asking if he still wanted to press charges.

Divens said he and Brooks were in touch and nearing a resolution. Two days later, Divens phoned the officer and told him he wanted to “drop it.”

“He said this would be bad for both of their careers and that he just wanted to keep playing and that they had resolved it,” according to the documents.

The officer told him the case would be referred to the DA’s office for review.

Contact Tracey Kaplan at 408-278-3482 and follow her at Twitter.com/tkaplanreport.