Writing in the British Medical Journal, James Barrett, consultant psychiatrist and president of the British Association of Gender Identity Specialists, claimed one in five doctors are reluctant to treat the issue.
Gender dysphoria is a condition where a person experiences discomfort or distress because there is a mismatch between their biological sex and gender identity, according to the NHS.
Mr Barrett said specific clinics for the condition were very busy and often patients were looking for hormone replacement therapy from their GP.
"Currently, however, in the experience of those of us who work at gender identity clinics as many as one in five GPs won't prescribe for people with gender dysphoria, even after expert advice from an NHS clinic," he wrote.
"Reasons that GPs have given me for this refusal include concerns about it being dangerous (it isn't), difficult (it isn't), expensive (it's not, particularly), and I've also heard disturbingly frank admissions that it was against 'deeply held Christian beliefs' or that 'we are trained to treat illnesses, not to change nature'."
In his article Mr Barrett claims that the General Medical Council had "made it clear that ethical or principled objections are not acceptable in gender dysphoria".
However, a spokesperson for the GMC referred Premier to its Good Medical Practice guide.
It states a doctor "must explain to patients if you have a conscientious objection to a particular procedure".
"You must tell them about their right to see another doctor and make sure they have enough information to exercise that right. In providing this information you must not imply or express disapproval of the patient's lifestyle, choices or beliefs," it adds.