lets face it, if the battery is so flat that it wont flash the indicators, then it certainly wont spin the starter motor or fire the ignition.
so, assuming that the battery is ok (youve got a multimeter right?) check the voltage with the bike standing and switched off, and again with the engine running. you will be getting 13-14 volts. if its just the indicators then you are looking at either, a duff relay, theyre easy and cheap to replace to check, cos even a duff relay might flash if it gets enough current, are the indicators bright when they come on or are they a bit dull? when they do flash is it quick or slow? do they flash on and off positively or just fade in and fade out? if you want to get to the bottom of this, then you need to give us all the information you can.
i assume the bulkbs are all clean and theres no connections loose or corroded, i also assume you have good clean earth connections(earths or the lack of are the cause of about 80% of electrical faults on jap bikes)
try and get some more information on it and we might be able to be more specific. you could have a duff switch on the bars, but without any more specific info we cant really do more than guess.