Lo Ping-cheng said in a weekly press briefing that Lin's resignation, tendered on April 4, will take effect on April 20.
Lo gave no indication as to who will take over Lin's position.
A Taiwan Railways Administration (TRA) Taroko express train crashed in Hualien on April 2, killing 49 people and injuring about 200, leading to harsh public criticism and demands for a TRA overhaul.