Can I refuse a specific medical treatment recommended by my doctor in Malta?

Yes, as a general principle central to informed consent and patient autonomy, you generally have the right to decline any recommended medical treatment, provided you have the capacity to make that decision, and a doctor cannot lawfully impose treatment on a capable adult patient against their genuinely informed wishes, except in narrowly defined and specific circumstances such as certain compulsory treatment provisions applicable under particular public health or mental health legislation in specific defined situations, which would not apply to an ordinary treatment decision like the one you're describing. That said, exercising your right to decline treatment doesn't mean the conversation ends there; a responsible doctor should properly explain the likely consequences of declining the recommended treatment, so you can make a genuinely informed decision, and continue to explore your concerns and any alternative options that might exist, since a good doctor-patient relationship should be able to accommodate your genuine right to decline while still ensuring you understand the implications of that choice. If you feel your doctor is not properly respecting your right to decline treatment, or is being dismissive of your genuine concerns rather than properly explaining the situation and exploring alternatives with you, it would be reasonable to seek a second opinion from another practitioner who may engage more constructively with your specific concerns.