It's meant to be psychosomatic I think.
Unfortunately I (STILL!!!!) have yet to read any of the books, so that's probably exactly what I'm missing.
Nah, the books are so different you can't really clarify anything in the movies based on them. Good books though (at least the first two), although dialogue doesn't seem to be Ludlum's strong suit.

He could hit his head when jumped from the boat. Amnesia doesn't necessary mean a heavy head/brain injury.

Yeah, it's this the unexpected presence of innocent, defenseless children in Wombosi's lap somehow short-circuited Bourne's brain. All the psychological training he'd gone through came crashing down and his mind just shut down.

Its the shock and trauma of being shot in the back and nearly drowning, from a physical point of view.
From a psychological point of view, it may well have been seeing Wombosi surrounded by his children. At that moment, Bourne suffered what might have been a psychotic breakdown of sorts where he 'rejected' his identity and repressed his memories (with the aforementioned shock and trauma helping along with that process).
As the series progresses, and he begins to re-orient himself with the secretive and violent world of his past, learns more about events in his past and encounters people he knew, he starts remembering more and more until in
Ultimatum
he
finally comes to terms with who and what he is, and why, and remembers everything.
Formerly sn939

Having watched Supremacy, and Ultimatum leads me to believe that his (Hidden in case you have yet to see the latter two)
"training" at the training facility is what caused him to lose his memory in Identity, and the first assignment he remembers is the murder of Mr. Neski in Berlin
.

Since there's no brain surgery or implication at all that he was shot in the head, I think you'd have to assume the movie uses the treatments as the cause of Bourne's amnesia. Perhaps the trauma of his experience on the boat added to it, but Treadstone messed with his head and then something went wrong. That's really all they give you.

I would highly recommend the first two books. But the story, after the beginning, is completely diffferent.

Oooo, Thanx alot!
The movie doesn't say anything about him being shot in the head. In the movie, he's shot twice in the back & then apparently falls into the water, but he hasn't even gotten any water into his lungs or anything by the time he's been rescued. Unfortunately I (STILL!!!!) have yet to read any of the books, so that's probably exactly what I'm missing. Now I understand. Thanx again!!
.

It wasn't completely clear in the movie, so I'm just going by the book here. But in the book, he'd been shot in the head, and floated in the water for hours before being rescued. He had both physical damage to the structure of his brain and a hysterical reaction to the lengthy trauma. In the book, he underwent some brain surgery to repair the damage, but his memory was never going to come all the way back. He would remember things in bits and pieces that he would have to piece together. But his hysterical memory loss was going to make his entire mind both reluctant to look at those bits and pieces and at the same time, obsessed with them.
But I should say that the movie was a huge departure from the book, and it's possible something different was intended.