The boy and his relatives were guests at the Cambridge Suites Hotel in the city's financial district, where officers were called just before 6 a.m., Det. Omar Khan said.
"The attending officers located a 12-year-old boy suffering from physical trauma," he said in a news conference.
"The victim was transported to hospital, where he succumbed to his injuries."
A male suspect was arrested at the scene but so far no charges have been laid, the detective said.
Police were tight-lipped about the investigation, saying they can't release much information because the victim is underage.
Khan told reporters he couldn't reveal the boy's identity under "police guidelines."
"All I'm going to release at this time is that it's a family situation," he said.
Hours after the incident, police announced that there was no threat to public safety and said "everyone involved is accounted for."