In recent days, some rumors have been circulating about the reasons behind the separation between Kojima and Konami, an unfortunate situation that is likely to only escalate as there still isn't any official explanation from either parties. As revealed by Rika Muranaka, the composer of MGS1-2-3's soundtrack (via NeoGAF), the reasons behind this split are of a financial nature.
According Muranaka, Konami wouldn't share any of the profits obtained from Metal Gear Solid's sales, and Kojima was given a fixed salary, regardless of the success of the games. In addition to this, according to Konami, Kojima would spend too much time and money for the development of Metal Gear Solid V: The Phantom Pain (to make the best game possible), with postponements and delays as a result, while he's continuing to receive his salary. This attitude would have annoyed the company and it leads to the split between the two.
Obviously, as we said earlier, it's a rumour and there's no official statement about that. It may not be the the only reason for the split either. We expect the proverbial Pandora's box to be opened when Metal Gear Solid V: The Phantom Pain will be available, on September 1st.