WASHINGTON — Five weeks after nine people were slain at a black Charleston church, federal authorities have indicted the suspected shooter on dozens of new charges, including hate crimes, firearms violations and obstructing the practice of religion.

The prosecution, particularly on hate crimes, has been expected since the June 17 shootings at Emanuel African Methodist Church in Charleston. The suspected shooter, 21-year-old Dylann Roof, is white and appeared in photos waving Confederate flags and burning or desecrating U.S. flags. He purportedly wrote online of fomenting racial violence, and federal authorities on Wednesday confirmed his use of a personal manuscript in which he decried integration and used racial slurs to refer to blacks.

The Justice Department has not decided whether it will seek the death penalty against Roof, nor whether its prosecution will come before a state case that includes murder charges and another potential death penalty prosecution.

Because South Carolina has no state hate-crimes law, federal charges were needed to adequately address a motive that prosecutors believe was unquestionably rooted in racial hate, U.S. Attorney General Loretta Lynch said.

Roof, Lynch said, had for months prior to the shootings conceived a goal of “increasing racial tensions ... and seeking retribution for perceived wrongs he believed African-Americans had committed against white people.”