The Oscar winning actress, her film star boyfriend Sean Penn and Jackson were enjoying a family day out at Vasquez Rocks in Santa Clarita, California.
During the trip, mum Charlize, 39, gave Jackson a 'time out' – the equivalent of putting him on the naughty step – which caused the little boy to have a screaming meltdown.
But a concerned hiker thought something more serious was afoot and started filming the crying boy.
According to TMZ, she then attempted to approach Jackson but was told by the actress to keep away from him.
The hiker then contacted the police and alleged she feared something bad could have happened to Jackson to cause him to be so upset.
Police arrived at the scene and it wasn't long before they established nothing was wrong, the website claims.
The website reported that Jackson looked like he was absolutely fine following the alleged incident, when Charlize was seen taking him to school in Los Angeles later that morning.
Charlize and her partner Sean arrived back in LA on Monday after spending months in her native South Africa working on the movie The Last Face together.
In 2012, Charlize spoke for the first time about juggling life as an Oscar winner with being a new single mum to Jackson, whom she adopted after splitting up with her partner of nine years, Stuart Townsend.
She said: "I've never felt more creative and with more energy but on the tiniest amount of sleep.
"I never knew I needed that little sleep. I always had eight hours and now it's, 'Wow, OK, you can function on just four'.
"But Jackson is great. I've always been very aware of balance and, even before I had a child, my life always takes priority to my work.
"I feel very blessed that I have this job but my job is not my life. I'm really lucky that I get to go and do this but my life is pretty kick-ass and I take real priority in that."