In most cases, you will have to buy your contraceptives with your own money, even if you obtain a prescription for free from a health centre GP. Unfortunately, there are no subsidy or reimbursement schemes for contraceptives in Malta, so they have to be purchased at retail price. If you have health insurance, check your policy to check what they cover.
A notable exception is you can get a hormone IUD inserted on the national health service if you have heavy periods. You may, however, still be asked to pay for the hormone IUD itself in such cases. There are also voluntary organisations like the Women for Women Foundation that can help fund contraception on a case-by-case basis for those who cannot afford it.