The Santa Clara County District Attorney's office had sought to charge Brooks with assaulting teammate Lamar Divens early last month but asked the court last week to put the matter on hold.
Sources told the San Jose (Calif.) Mercury News there was some indecision within the prosecutors' office over whether the case should be considered a felony or misdemeanor.
Brooks allegedly hit Divens with a beer bottle and punched him during a daylong drinking spree in San Jose. Divens needed three stitches and had agreed to press charges, but later changed his mind, the warrant application said.
Police took a report on the scuffle at the time but did not arrest Brooks, the newspaper said.
Brooks, 29, last year signed a six-year contract extension with the 49ers.