The organisation fears new guidance from the industry regulator would see believers forced to dispense abortifacient drugs, such as the morning after pill, or hormone blocking drugs used by transsexual patients.
Speaking ahead of the end of a consultation period on the guidance next week, Chief Executive Office Dr Peter Saunders described the plans as "draconian", "unethical, unnecessary and quite possibly illegal".
He went on to say: "For the sake of professional freedom and reasonable accommodation, essential in a pluralist multi-faith democracy, let's hope that they choose instead a more flexible, tolerant, respectful and eminently sensible path."
Take part in our #consultation on #religion, #values and #beliefs >> https://t.co/sb3iWLBjai #ValuesBeliefs pic.twitter.com/uXP44Kb5Dw
— GPhC (@TheGPhC) February 16, 2017
Proposals by the General Pharmaceutical Council (GPhC) state pharmacist must not "impose" their beliefs and values on other people.
It also says that pharmacists must "take responsibility for ensuring that person-centred care is not compromised because of personal values and beliefs".
In the consultation document, the GPhC said: "These proposals will change the expectations placed on pharmacy professionals when their religion, personal values or beliefs might - in certain circumstances - impact on their ability
to provide services.
"They will shift the balance in favour of the needs and rights of the person in their care."
Dr Saunders warned the guidance could see pharmacists "pressured to comply or risk disciplinary procedures and/or possible loss of employment", while potential trainees could be "dissuaded" from pursuing a career in pharmacy.
Meanwhile, pro-life campaign Chris Whitehouse from Right to Life recently warned the proposed new guidance could contravene the Equality Act 2010.