The singer caused a stir when he appeared with the child in Berlin, precariously clutching the infant out of a third floor window, and draping a towel over the baby's head.
"I got caught up in the excitement of the moment. I would never intentionally endanger the lives of my children," Jackson said.
A spokesman for the Bambi entertainment award ceremony, where Jackson is due to receive a lifetime achievement award, told the Associated Press news agency the child was Jackson's youngest son Prince Michael II.
Rumours have been circulating for months that Jackson has a third child, but it is not yet known if the child is adopted or is his biological offspring.
About 200 fans gathered at the entrance to the Adlon Hotel, near the Brandenburg Gate, as Jackson's motorcade arrived on Tuesday.
The reclusive performer had to fight his way through the crowd of fans to get into the hotel, in a scrum that injured one person.
Safely inside
Later, Jackson dangled the baby out of the window of his room on the third floor, holding it with one arm under its shoulders.
Many onlookers feared the 44-year-old would drop the infant, although he brought the child back inside safely.
As fans cheered for him to appear again, Jackson came out onto the balcony covering his face and threw a towel down to the crowd below.
Jackson has two other children, Prince Michael, who is five, and Paris, who is four.
The singer's close friend, psychic Uri Geller, condemned Jackson's actions but did not believe he was capable of harming a child.
"I just would not put any child over a railing at such a height," he said.
"I think it was a silly thing to do. He probably did it because he was overwhelmed emotionally by the fans."
But he had suspected the baby was a fake, saying he was "too protective" of his children to do something like this.