The News Agency of Nigeria reports that over 1,000 people went home disappointed as they could not secure seats on the train.
The NRC had on October 28 announced the special transit service for the Eid-el-Kabir scheduled for this weekend.
The corporation announced a fare of N180 for economy class passengers on Lagos-Abeokuta route of about 97km while passengers on Lagos-Ilorin route pay N680 and N1, 010 for economy and first class respectively.
NAN also reports that the first train of 10 coaches left at about 9.30am with scores of passengers seen standing and lapping themselves, while the second train left at noon.
Passengers, who spoke to NAN, lauded the intervention of the corporation, while those who could not make the trip, criticised what they called "poor arrangement" by the officials.
One of the passengers, Mr. Mustapha Adisa, said the special train service afforded him the opportunity of taking his entire family to Ede, Osun, for the Eid-el-Kabir celebration.