Aberdeen was actually one of the main stars of the film it seems because the same location is used several times to portray different places. At the beginning of the film it is supposed to be some anonymous port on the Indonesian island of Java, and then later, with a bit of jiggery pokery (some footage of a train superimposed in the background) it gets turned into the fictional post of Batu Kring from where Jim starts his epic up river mission.
In the top picture you can see the promontory that houses the seminary (look closely and you can just make out its roof) with Brick Hill in the background. The second picture shows both the Tai Pak and Sea palace moored in the middle of the harbour.
Later in the film we get the shot below - essentially taken from the same point as the second picture above, but without the zoom, but notice that there is a trail of smoke at the back. This is actually the superimposed train. From the looks of it everything front and middle is real but the far distant shoreline has been manipulated. It's quite convincing for a film shot so long ago, but the big giveaways of course are not only the still obvious floating restaurants in the middle of the harbour, but also the obvious presence of the old Police Station on the hill on the right. This is a great shot of the building because 1963 was obviously a time before any high rises had been built along that part of Aberdeen Praya Road. I'll do a separate post later where the film used those low rises with a closer angle.