While Tesco has apologised, it says the pharmacist was acting within his rights under an industry code of ethics.
Ruth Johnson, 30, whose youngest child was born four weeks ago, had not been using her usual contraception with her fiancé and asked for the pill Levonelle at her local Tesco.
She said: 'The pharmacist ... told me that he would not be "allowing" me to buy the pill from him, because he had a right to refuse to sell it on the basis of his personal beliefs.
'The pharmacist was of Asian origin, so I asked him if it was because of his religion and he replied, "Yes."'
Following the incident Johnson, of Cleethorpes, complained to the store manager.
She said: 'I was told that it had nothing to do with them and that they couldn't force the pharmacist to sell it, despite him working in their store.
'I then asked if a Jewish or Muslim checkout operator could refuse to sell pork or alcohol, or if a Jehovah's witness could refuse to sell birthday and Christmas cards.'
A Tesco spokesman said the pharmacist advised Johnson on other places to purchase the pill, but was acting within his rights to refuse to dispense it himself.
He said: 'We do apologise to Miss Johnson for the inconvenience caused.
'However, the Royal Pharmaceutical Society's code of ethics allows pharmacists the right to refuse.'
Johnson, who thought the supermarket service would be more discreet than a local chemist, said she feared for any teenage girls who might be turned away from seeking the morning-after pill, Daily Mail reports.
She added: 'I appreciate we live in a multicultural society, but what gives him the right to impose his beliefs onto me?'
A spokesman for the Royal Pharmaceutical Society of Great Britain (RPSGB) said: 'The Code of Ethics and Standards does not require a pharmacist to provide a service that is contrary to their religious or moral beliefs.'
But he added: 'Any attempt by a pharmacist to impose their beliefs on a member of the public seeking their professional guidance - or a failure to have systems in place to advise of alternative sources for the service required - would be of great concern to the RPSGB and could form the basis of a complaint of professional misconduct.'