Bad News For The Digital Newsstand: Apple Rejects Sony Reader App

Here’s one that will have the Apple (NSDQ: AAPL) watchers puzzling for the next day: Apple has reportedly rejected Sony’s Reader app from its App Store because it sells content within the app, and lets users access content that they purchased outside Apple’s own App Store. The news comes one day before Apple is supposed to take the stage with News Corp (NSDQ: NWS). to debut the new digital magazine The Daily.

According to The New York Times, which first reported the Sony (NYSE: SNE) story, Apple has told Sony that from now on all in-app purchases have to go through Apple.

The Sony Reader Store is designed to work both with Sony Reader devices and third-party hardware. Installed on other devices, such as an iPad, the Sony Reader app acts as a digital locker and lets users access their e-books, magazines and newspapers, as well as purchase more content.

The move throws into question what might happen with similar digital reading apps, such as the popular Amazon’s Kindle store. Like Sony Reader, the Kindle store is designed both to use with Amazon’s Kindle devices as well as third-party products for which the Kindle app is available. Up to now, users have been able to use the Kindle app to read already-downloaded/purchased content; as well as buy new publications.

There has been a lot of speculation over what Apple is planning to do in its next iteration of the app store, and this might be giving us a hint at what direction it hopes to go. Last month, when reports surfaced that Google was gearing up to develop its own “digital newsstand” for Android devices, there was also talk of Apple looking to revamp how it lets app publishers charge for content as well.

Up to now, there seems to have been a very mixed — and frankly confusing — in-app charging policy:

Not only does the Kindle app already allow what the Sony Reader app was trying to put in place, but when it comes to individual publications, there is no consistency (unlike old-fashioned paper mags which have very obvious and consisten purchasing channels). Some apps such as Newsweek‘s and the Economist‘s do offer subscriptions, but the norm seems to be paying for single issues, which means users have to keep returning to the iTunes store to keep reading.

But what is clear is that Apple has wanted to be the lynchpin when it comes to transactions in apps, routing all purchases through users’ iTunes accounts. It may well be that Apple plans to put more purchasing power and flexibility into its own system, and will be asking third parties like Sony to fall in line.

Or it could be, as it was with Google (NSDQ: GOOG) Voice in the past, just one of those examples of a rejection later overturned for reasons we can only guess.