Following last night’s report on Apple signing a deal with the third music label, Sony, over the launch of the rumored iTunes cloud service after inking similar agreements with EMI and Warner Music Group, Peter Kafka at All Things Digital reports negotiations won’t be over once Apple also signs Universal, the biggest music label in the United States; whilst Apple is clearly in advantage when compared to Google and Amazon thanks to its music deals, the company still has to finalize agreements with music publishers, which own different rights on songs and albums than labels. As Kafka explains, publishers are different entities, usually shared within the same label but still residing in separate buildings, that own rights to the songs’ compositions, as opposed to the labels who own rights to the recordings. Once music is distributed either physically or online, both get paid with different fees and terms; once example is the Beatles music catalogue, with recordings owned by EMI and compositions by publisher Sony/ATV.

Kafka claims Apple simply started negotiating with the labels first, and deals with publishers are currently being worked on ahead of a rumored WWDC launch.

While Apple came to terms with Warner Music and EMI Music weeks ago, and has now struck a deal with Sony Music, industry sources tell me the company doesn’t have agreements with labels’ associated publishing companies — Warner/Chappell, EMI Music Publishing and Sony/ATV. The deal Apple is about to sign with Universal, also won’t include publishing, I’m told.

Music industry sources I talk to think Apple wants to launch, or at least announce, the cloud service at its developers’ conference in early June. And if the hang-up is truly just about money, then that still gives dealmakers time to hammer things out. But remember that this is the music business, and simple things always take longer than they should.

As reported several times in the past few weeks, Apple’s upcoming cloud-based music service is rumored to offer both uploads of a user’s music collection and access to songs not previously purchased, but available for streaming through a subscription system.

As work on the rumored cloud music service nears finalization for an official WWDC announcement, Bloomberg reported last night Apple has reached a deal with Sony Music Entertainment, following reports that the company managed to sign the Warner Music Group and EMI. This leaves Universal, the biggest label of all four in the United States, out of the equation, but according to the rumors Apple’s Eddy Cue is actively focused on closing all the remaining paperwork with music labels by next week.

Apple has reached licensing accords with Sony Corp. (6758)’s music division, EMI Group and Warner Music Group, the people said. Universal Music Group, the largest recording company, is close to a deal, another person said. The company also would need to reach agreements with music publishers, which control different rights than the labels.

Apple’s cloud music service is said to be part of a major MobileMe revamp the company has been working on for the past two years, which will include several new functionalities and a new price point with basic features offered for free. As for the music service, it’s unclear whether Apple will adopt an upload system like Google and Amazon or a subscription-based delivery with songs coming from the iTunes Store, but a patent surfaced yesterday seems to suggest Apple’s implementation will go as far as allowing users to upload their own songs, and stream others they don’t own from a larger “content source” like the iTunes Store.