The hearing was suspended before a decision could be filed, as spectators overturned courtroom tables and tossed chairs.
Relatives left the court and marched towards the company's headquarters, where they lit fires and skirmished with the police for several hours.
Scattered protests faded after nightfall as police chased away youngsters. About 40 protesters were arrested.
The public court hearing was held at a converted basketball court to accommodate the victims' relatives.
The session, one of several public hearings over the past four months, was immediately halted by the disturbances.
About 35 police officers escorted the three judges to safety beneath plastic shields.
One judge said she favoured a more severe murder charge, while two judges arguing that manslaughter charges should be applied against the three defendants - reasoning that the supermarket's doors were not shut in a wilful attempt to kill.
A manslaughter conviction could carry a penalty of up to seven years in prison, while prosecutor Edgar Sanchez complained that a murder charge should be applied as it would be punishable by at least 25 years in prison and restitution to victims' families.
|Pio Paiva, right, owner of the supermarket that |
went ablaze in 2004 killing about 400 people
Nicanor Duarte, the president of Paraguay, went on television and appealed for calm after 15 demonstrators and 12 police officers were reported injured.
He said he had asked for the three-judge panel to be removed from the case.
"I've spoken with the attorney general of the nation and have asked him with all due respect to request that these judges be removed from this case," Duarte said.
The August 1, 2004, fire killed 432 people, most by asphyxiation, as thick smoke swept through the supermarket in Asuncion.
About 2,000 people were in the building, many of them families with children.
Prosecutors argue that the doors were deliberately ordered shut to prevent looting, trapping many inside.
Juan Pio Paiva and son Daniel Paiva, owners of the chain, were arrested soon after the fire along with a store guard whom many relatives wanted to face murder charges.
The relatives and their supporters said they were angry over what they called a lack of justice in the case.