It costs a lot of money to make coins. With inflation appearing to always be just around the corner, the government if afraid of investing tons of money to mint coins that could some become worth significantly less than the metal they're made of.
That is true. May be the govt should print notes for minor denominations too. They are the government they can legally launch a new currency note, can't they ?
The govt seems to be losing a lot more money with the shortage, like people forced to give free rides on subway.