The charges relate to a party that Smith had at his home on June 29, 2012, where a Northern California man alleged that he was shot, naming both Smith and his former teammate Delanie Walker in a lawsuit filed last month.
The 49ers released a statement acknowledging that they are aware of the charges, but refused to go into any further detail due to legal reasons.
"The 49ers organization is aware of the recent developments with Aldon arising from an incident at his home in 2012," read the statement.
"We recognize the serious nature of this situation, as does Aldon, and will continue to monitor it closely. As this is an ongoing legal matter, we will have no further comment."
Smith is currently on indefinite leave from the team while he undergoes treatment for substance abuse following a DUI arrest last month.