Three people were killed on the spot, while two others, including a three-year-old child, were rushed to hospital, where they were declared brought dead, sources said.
The accident occurred around 3:00 pm, according to the sources.
According to eyewitnesses, the car was hurled 100 metres away in the impact of the collision.
On hearing the deafening noise, people from nearby areas rushed to the spot to commence rescue operations.
Protesting against the railway authorities, the agitated people did not allow the train to leave for some time. However, the train later left for Tirunelveli, railway sources at Kochi said.
Reports say the Kochi-Alappuzha stretch has a string of unmanned level crossing and several accidents have occurred in the same area in the past. In 2010, four holidayers, including a foreign couple, were killed when their car was hit by a train at an unmanned level crossing at nearby Mararikkulam.
After today's accident, state Transport Minister Aryadan Mohamed stressed the need to set up manned level crossings, which should be taken up with the Centre.
Though this issue has been brought to the notice of the Centre several times, no solution has been found, he said.
The minister also wanted Railways to provide adequate compensation to the families of the victims and said the state would also extend immediate relief to them.