LIRR canceled 12 westbound trains and there were systemwide delays of five to 10 minutes for most of the morning.
"I have a car so this is my only way to go," said commuter Eric Wison. "If the schedule changes too much, then I guess I'll have to take the bus."
LIRR's crews worked overnight to try to repair damage to switches and tracks caused by the Sunday's derailment, but work was not completed in time for the Monday morning rush hour.
The derailment happened when four cars of a Huntington-bound train went off the tracks, just west of the Jamaica stop. No one was injured.
On Monday morning, three of the cars were still off the tracks. After they're removed, experts will assess the damage to the tracks.
The railroad serves about 110,000 customers during the morning rush hour, most of them heading for New York City.
Evening rush-hour service could also be affected, railroad spokesman Rich Mendelson told Newsday .
Sunday's derailment marks the second major LIRR incident in less than a week. Service was disrupted for several hours after two trains bumped into each other as they were departing Jamaica Station on Wednesday. Two people suffered minor injuries.