What OSes are common on mobiles?

Are iOS(iphone) and Android the common operating systems on smart phones in Japan or are the majority of Japanese mobile phones still on their own OS?

I know the models are way different but I was hoping some of the JP carriers would have Android OS phones. As of now the only phones I know for sure have Android OS in Japan are some of the HTC phones.

iOS and Android are both very common...
Android OS is offered by a wide variety of makers including japanese makers. for example check au lineup they have many android devices...
http://www.au.kddi.com/seihin/ichiran/smartphone/

Are iOS(iphone) and Android the common operating systems on smart phones in Japan or are the majority of Japanese mobile phones still on their own OS?

iOS and Android are both extremely common. All major carriers have several android devices (made by sony, htc, panasonic, casio, etc.) and both Softbank and Au have the iphone. Windows Phone devices also available. Overall though, most Japanese mobile phones are probably still running proprietary os's.

Here's the english pages of the major carriers:

docomo:
http://www.nttdocomo.co.jp/english/

softbank:
http://mb.softbank.jp/en/

au:
http://www.au.kddi.com/english/

The age of the Galapagos mobile phone is drawing to an end. This year should see more Android phones on the market than proprietary phones.

The last time I checked, Android handsets accounted for around 80% of the smartphone market in Japan, and smartphones were over 50% of the mobile phones sold.

Yeah you say "I know the models are way different" well that way of thinking is maybe a little out of date, that used to be the case until the iPhone came along...even at first some people doubted that the special Japanese market would accept the iPhone. As it turns out the iPhone is totally dominating the market...the Japanese clamshell devices just seem old technology in comparison and Japanese customers love new technology.
lots of those "special functions" for the japanese market like QR code reader and emoticons etc can be achieved with apps, so there was no contest really. Just up until about 5 years ago the phone market was very exclusive and closed off to the outside world. AU, softbank(when it was vodafone?), docomo etc only sold devices by Japanese manufacturers...thats all changed now. You will see many handsets from non-Japanese manufacturers such as LG , HTC, Apple, Samsung etc so it is not so different to other countries. Expect to see the same thing happen with TVs in the next few years (it is still fairly Japanese only) despite brands like Samsung being hugely popular for TVs all over the world trying finding one in your local Yamadadenki. Apple are in a position to change that...they have done it before. Once Apple are in the rest will follow.