Cars were set on fire and a local convenience store was also damaged, police said.
The protest followed a peaceful vigil for the victims of a deadly stabbing that occurred a day prior in the town.
Three children were killed and nine others injured in the stabbing incident, police said. Two adults were also injured while trying to protect the children, police said.
Merseyside police said the children were attending a Taylor Swift-themed event at a dance school at the time.
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A 17-year-old boy from Banks, a coastal village in Lancashire, just outside Southport, was arrested on suspicion of murder and attempted murder, police said. The suspect, whose name was not released, was born in Cardiff, Wales, police said.
The motive remains unclear, police said.
Tuesday’s protests were apparently fueled by “speculation” over the unidentified suspect, Merseyside Assistant Chief Constable Alex Goss said.
“There has been much speculation and hypothesis around the status of a 17-year-old male who is currently in police custody and some individuals are using this to bring violence and disorder to our streets,” Goss said in a statement. “We have already said that the person arrested was born in the UK and speculation helps nobody at this time.”
Goss said protesters used bricks to attack officers and damaged cars parked in the mosque parking lot. Officers sustained injuries including fractures, cuts, head injuries and a concussion, police said.
“This is no way to treat a community, least of all a community that is still reeling from the events of Monday,” Goss said.