An article at Japanese financial newspaper Nikkei (in Japanese) outlines some of the troubles and (if true) alarming working conditions at the famed developer and publisher. According to one person in the article a change in culture happened when a low budget mobile project (Dragon Collection) became a big hit in 2010. After that, Konami leadership was unwilling to invest larger sums in risky console projects. Furthermore there are reports of rather harsh and strict working conditions where a punch card system is employed and staff who go on what is considered too long lunch breaks are "outed" to the rest of the company. E-mail correspondence with outside parties is done via randomised e-mail addresses that are regurlarly changed. Developers who are deemed as undesirable are forced to do menial work duties such as cleaning gym areas, do security guard work, or work the assembly lines at Konami's pachi-slot manufacturing. Apparently, liking a Facebook post of a former colleague saying he's left Konami for another company would be enough to warrant a reassignment. Many influential developers have left and development of the classic franchise Suikoden has been put on hold.
At then there's Hideo Kojima. According to the article the development budget of Metal Gear Solid V: The Phantom Pain (as of April) had ballooned to more than $80 million. The constant delays and increased costs put Hideo Kojima out of favour with management.
Thanks to translator Thomas James - whose tweets on the matter can be found here.