Hello,
I am indian citizen born in kathmandu , nepal and having valid birth certificate from hospital for having birth place as kathmandu nepal. In my indian passport, even my place of birth is kathmandu, nepal and we have registration card from indian embassay at kathmandu that we are staying at nepal.
But as such i dont have birth registration from embassay of in kathmandu, wanna know whether i could get birth certificate from govt of nepal at present which is required for filing GC in usa for chargeability under nepali citizen.

I don't think you will get birth certificate from government of nepal since you are not Nepal citizen. Nepal does not provide citizenship based on birth alone.
The best bet would be to try to use the birth certificate from hospital.

It's just my guess. I might be wrong.