You only ever receive one in every game. But I would suggest Dusk Balls if you're trying to catch the rest of the legendaries. I still haven't used my Master Ball but the largest number of Dusk Balls I've even had to use on one Pokemon was Zygarde, which took me only 3 attempts. Dusk Balls are $1,000 each.
In BW/B2W2 there was a second way (forgot how, but i do know I have two unused master balls for each, in case I ever found a shiny). One I believe was given by Professor Juniper and the other from Colress. Now, as for X/Y, I'm not sure if you can get another one, I haven't found a second yet :).