The tribunal ruled Canon Jeremy Pemberton was not discriminated against when the Church stopped him from taking up a new post as a hospital chaplain after he married his same-sex partner.
He plans to appeal against the ruling.
A Church spokesman said the CofE "remained engaged â€¦ in exploring questions relating to human sexuality".
Mr Pemberton, who married his partner in Nottinghamshire in April 2014, alleged the Diocese of Southwell and Nottingham's stance on same-sex marriage breached the 2010 Equality Act.
He said: "The Church is too frightened to deal with this case head-on because the leadership knows full well that most people in the pews think that their attitudes are outmoded and wrong.
"Some clergy are marrying secretly because they are worried about what the Church might do to them - and that is an extraordinary idea in the 21st Century."
He said Church rules were contradictory as he is still a priest of good standing in Lincolnshire, where he continues to work as a hospital chaplain.
Theologian the Rev Ian Paul welcomed the tribunal's decision as "a breath of fresh air", which reiterated the freedom of the Church to decide its doctrine.
"It would have been a curious situation if the Church had to bow to what the current view of culture and society and law wasâ€¦ if the tribunal had gone with that it would have had very serious implications," he said.
The Church's decision not to issue a licence to officiate in the Southwell and Nottingham diocese meant Mr Pemberton was unable to take up a post as a bereavement manager at the Sherwood Forest Hospitals NHS Trust.
Gay rights campaigner Peter Tatchell said: "I think he had a strong moral and ethical case... and it causes me considerable pain and distress that the Church of England  is still enforcing discrimination against gay clergy."
A gay clergyman who lost an employment tribunal against a diocese says he will continue to fight "outmoded and wrong" attitudes in the Church of England.