Authorities said on Monday they were trying to relocate the container, which was rented after mortuaries in the city of Guadalajara became full.
"We have a lot of children in this neighbourhood... it could make us all sick," resident José Luis Tovar said.
Laws in Mexico prevent the cremation of bodies linked to violent crime.
Local authorities said they were looking for a longer-term solution to store the bodies following a recent wave of violence.
"We ran out of cemetery plots where we could bury them," the head of the Jalisco forensic investigators unit, Luis Octavio Cotero, said.
He added that a site was being established that was expected to facilitate some 800 corpses, AFP news agency reports.
The refrigerated trailer had previously been parked at a warehouse in the neighbourhood of Duraznera, on the outskirts of Guadalajara, but after two weeks the residents began to complain of a foul stench and said the container was attracting flies.
It was then moved to an empty lot in the suburb of Tlajomulco de Zúñiga, but residents there began to protest at the weekend.
"We don't want it here. They need to put it somewhere else, it stinks," Mr Tovar said.
Mexico has suffered a wave of violent killings in recent years.