Police believe Sebastian Rios and his mother, 24-year-old Yasemin Uyar, were abducted by the boy's father.
Police said the suspect is 27-year-old Tyler Rios of Highland Park.
AMBER Alert notifications were sent at around 2:40 p.m. Friday.
The Union County Prosecutors Office is leading the investigation, but has not released other details.
CBS2's Jessica Layton reported about Rahway police officers have been investigating around a home on Westfield Avenue, where neighbors said Sebastian and his mother live.
Authorities seemed to be zeroing in on a staircase on the side of the house leading up to a second-floor door, but they have not said anything about the significance of that area of the home yet.
There was police tape around the entire block.
Neighbors said they don't know the dad, but they've seen Uyar and Sebastian around the neighborhood and at the local soccer field in the past.
The community is worried sick about the young mother and her son.
"Oh my goodness. That is just unconscionable, unimaginable," said neighbor Sharon Watkis. "I can't imagine what could have happened, but I pray to God that wherever they are, or whoever took them, I pray that they be found safe and sound."
"My heart is devastated. I'm just praying that they're found safe," said Sharon Myers.
"[They're] probably scared to death. I'd be so scared," one neighbor said.
Friday evening, a new alert went out with updated information on the license plate of the car.
Police believe Rios may be driving a silver four-door Ford Fiesta with New Jersey license plate W421713, which is different than the license plate that went out with the initial AMBER Alert on Friday afternoon.
Anyone with information on their whereabouts should call 911 or the Rahway Police Department at 732-827-2200.
CBS2's Jessica Layton contributed to this report.
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