Cars were burned in Moirans as dozens of protesters vented their anger at a judge's decision to deny a young man leave to attend his brother's funeral.
Mr Valls condemned the "unacceptable violence" and demanded "extreme firmness" in dealing with rioters.
No-one was hurt in the violence but the disruption halted local train services.
The railway line at Moirans between Grenoble and Lyon was cut and a main road in the Isere area was also blocked by burning cars.
The prime minister said those involved would be pursued relentlessly.
The funeral went ahead on Wednesday afternoon, reports said, days after the young man was killed in a crash involving a stolen car. Two other people died in the accident.
Adele Vinterstein, whose son died in the crash told news channel iTele she simply wanted her other son to be at his brother's funeral.
But repeated legal attempts to enable him to leave prison temporarily were turned down, with or without an escort.
"I just don't understand why they won't let him out. He's not a paedophile, he's not a thief, he's not a killer. My son's not a dog," Ms Vinterstein told reporters. "It was his right to say goodbye to his brother and give him a final kiss."
She appealed for an end to the violence, saying that burning cars did not help.
The riot came less than two months after another traveller community in northern France blocked a motorway, when authorities refused to temporarily release the son of a shooting victim to attend his father's funeral.
In France around 400,000 people are officially classed as travellers and Roma (Gypsies), but the number is believed to be far higher.
Prime Minister Manuel Valls has promised a tough response after members of a community of travellers went on the rampage in south-eastern France.