The Rialto crash was far less serious than the catastrophic head-on collision in September between a Metrolink train and a Union Pacific train in Chatsworth that killed 25.
Five passengers aboard the Metrolink train were sent to area hospitals with complaints of pain, said Lt. Joe Cirilo of the Rialto Police Department.
It was unclear who was at fault.
Lena Kent, a spokeswoman for Burlington Northern, said her railroad's engineer had been given the go-ahead either by a signal or a Metrolink dispatcher.
"We were cleared to go into the siding," she said. "It had almost cleared the mainline [track] when it was struck."
Metrolink declined to comment other than to say it was investigating what went wrong.
"No matter what happened, it's not acceptable," said Keith Millhouse, vice president of the Metrolink board and a Moorpark city councilman. "We'll have to figure this out. I have a zero tolerance for any type of incident, no matter how minor it is."
Investigators in the Chatsworth crash have focused their probe, in part, on why the Metrolink engineer missed a crucial red signal to stop the train.
Officials have not said whether the Metrolink engineers in Thursday's accident missed a signal.
A spokesman for the National Transportation Safety Board said investigators from the agency's regional office in Gardena were at the accident scene. The Federal Railroad Administration also dispatched investigators.
"The contact between the Metrolink locomotive and the freight train is characterized as a minor sideswipe, not head-on, with no attendant damage to passenger coaches or freight cars, nor to track and signal facilities," Metrolink said in a statement.
Thursday's crash, like the one in September, happened on a stretch of track owned, maintained and dispatched by Metrolink.
The freight train was en route from Barstow to Rialto, said Kent, the Burlington Northern spokeswoman. She said the Metrolink locomotive struck the 96th car of 102 cars on the train and slightly damaged the last few cars on the train.
Barry Sweedler, who spent 30 years as an NTSB investigator and administrator, said the number of accidents involving Metrolink trains is getting attention in rail circles.
"This is reaching a point where it's more than happenstance," he said. "It just seems like there's too many situations here that need to be cleaned up."
In the September crash, the Metrolink engineer was alone in the locomotive. The NTSB has said that the engineer was text-messaging on his cellphone in the seconds before the crash.
In response to that crash, there were two engineers aboard the Metrolink train Thursday. It was in the "pull" mode, meaning that the locomotive was at the front of the train.