Dr David Mackereth claimed he was sacked after saying he would not “call any 6ft tall bearded man madam” during an “abstract discussion” with his manager.
But a tribunal panel unanimously concluded the “lack of belief in transgenderism and conscientious objection to transgenderism in our judgment are incompatible with human dignity and conflict with the fundamental rights of others, specifically here, transgender individuals”.
Publishing its conclusions, the tribunal panel said: "In our unanimous judgment there was no contravention of part 5 of the Equality Act 2010 and the claimant was not subjected to discrimination.
“Those complaints are dismissed.”
Dr Mackereth has said he will appeal the decision.
In his witness statement to tribunal hearings in July, Dr Mackereth said that transgender individuals “may find my views to be offensive”.
Dr Mackereth, who was trained to assess eligibility for Employment Support Allowance or the capability element of Universal Credit, also said there was no deliberate desire on his part to offend people.
But the tribunal “found that his beliefs were likely to cause offence and have the effect of violating a transgender person’s dignity or creating a proscribed environment, or subjecting a transgender person to less favourable treatment”.
As well as claiming religious discrimination, Dr Mackereth said no effort was made to accommodate his beliefs, such as referring transgender clients at Birmingham’s Five Ways assessment centre to another doctor.
Responding to the judgment, Dr Mackereth, who now works as an emergency doctor in Shropshire, said: “Without intellectual and moral integrity, medicine cannot function and my 30 years as a doctor are now considered irrelevant compared to the risk that someone else might be offended.
“I believe that I have to appeal in order to fight for the freedom of Christians - and any other NHS member of staff - to speak the truth.
“If they cannot, then freedom of speech has died in this country, with serious ramifications for the practice of medicine in the UK.”
Andrea Williams, chief executive of Christian Legal Centre, said: “This is an astonishing judgment and one that, if upheld, will have seismic consequences not just for the NHS and for Christians, but anyone in the work place who is prepared to believe and say that we are created male and female.”
A DWP spokesman said: “We acted to protect claimants from behaviour that would have failed to treat them with dignity, so we welcome this ruling.
“We expect all assessors to approach their work sensitively.”
Press Association contributed to this report.
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