Is a govt employee entitled to get stipend when studying

I have got an appointment in Kerala state government and i took study leave (leave without pay for continuing higher studies, since i havent completed probation) through Kerala government as soon as i joined. The same i have intimated in my studying institution that I will be taking leave for higher studies as soon as i join. I got sanction order from Kerala government as well to continue my higher studies. But in my institution it is told that i cant get stipend/fellowship because still i m an employee of Kerala govt and i cannot be given fellowship from the above said institution(under central govt). But I got sanction order clearly stating loss of pay and permitted for higher studies. Could you please let me know whether am I eligible to get stipend or not?