Jesse was not hurt in the incident, during his family holiday on the privately-owned St Tudwals island, Wales.
Grylls, known for his television expeditions and survival skills, had contacted Abersoch RNLI to ask whether they wanted to use the area, Half Tide Rocks, for their weekly training mission.
A spokesman later claimed they had not been fully aware of the live risk of the practice rescue, saying: "In hindsight, the child should not have been on the rocks."
RNLI manager Gareth Hughes said: "The crew tell me they didn't know Bear's son was going to be on the rocks as there is an element of risk.
"I certainly wouldn't put my young son on those rocks."
Mr Hughes was on holiday at the time, and came home to discover the practice mission had involved a child.
He added: "Thankfully, no one was hurt but in his efforts to give the RNLI some publicity this is the wrong kind.
"As I understand it, it was supposed to be a low key exercise and I believe no photographs were supposed to be taken.
"But this could also encourage people to do the same which would be unfortunate."
Grylls has since deleted his public tweet, which read: "Jesse and the @rnli on a training exercise to rescue him off the rocks!"
He is a celebrity ambassador for the RNLI, previously saying: "I am so proud to be an ambassador for the RNLI and full of admiration for all their work."
An RNLI spokesman said: "Bear Grylls had approached Abersoch RNLI and asked if on our normal Thursday training evening, we could do an exercise with him.
"We did not appreciate that the exercise would involve him putting his son on Half Tide Rocks.
"Bear Grylls put his son on the rocks and then the lifeboat, as part of the exercise, rescued him from the rocks.
"In hindsight the child should not have been on the rocks but everyone was acting with the best of intentions and getting valuable practise in rescuing a child."
They later clarified they were "very grateful" for Grylls' work as an ambassador for the charity, adding of the incident: "The lifeboat and its crew was in close attendance and the boy was in sight at all times and wearing a life jacket."
The spokesman said Abersoch RNLI launched 15 times in the last three weeks and some of the rescues involved children. Last year a third of all those rescued by Abersoch were under 18.
Half Tide Rocks is home to a seal colony and is a treacherous area for yachtsmen hitting them when they are covered by the incoming tide.
On stormy days huge waves breaking over the rocks can be seen from the mainland.
Earlier this year, the adventurer was criticised for taking sons Jesse, Marmaduke, eight, and Huckleberry, six, on a powered paraglider without safety helmets.
Speaking of his children at the time, he said: "Nothing in this world matters more to me than keeping them safe whilst also helping them to have fun.
"I always try though to help them learn how to manage risks effectively, and understand where the danger always comes from."
A representative for Grylls, who is an ambassador for the RNLI and also , has been approached for comment.
- Daily Telegraph
