"They failed to immediately alert the authorities after the incident, which led to a tragedy... that caused massive damages and shocked the international community."
Li, 49, was part of a contracted railway maintenance team that regularly inspects Taiwan's mountainous eastern train line for landslides and other hazards.
His assistant, an undocumented migrant worker identified only as Hwa, and two Taiwanese supervisors of a construction site near the track were also charged with negligent homicide.
The offense is punishable by a maximum of five years in jail, prosecutors said.
Li faces an extra charge of fleeing the scene after the incident, which is punishable by a maximum of seven years in prison, they added.
Taiwan's transportation minister Lin Chia-lung has tendered his resignation over the train crash, which plunged the island into mourning.
The last major train derailment in Taiwan was in 2018 and left 18 people dead on the same line. The train driver was later charged with negligent homicide.
Taiwan's most deadly rail disaster on record was in 1948 when a train caught fire and 64 people perished.