The agencies said the law went against the Church's teachings
Half of the Roman Catholic adoption agencies who warned they would close rather than allow same-sex couples to adopt will now abide by the law.
The agencies were given an 21-month exemption from the anti-discrimination laws, which came into effect in 2007, but that expired on 1 January.
They said the law, which makes it illegal to discriminate against gay applicants, went against their beliefs.
Five of the 11 agencies will now comply with the rules, while one is to close.
When the Equality Act became law in April 2007 in England, Wales and Scotland, it banned discrimination against homosexual people in the provision of goods and services, which incorporated adoption agencies.
The BBC's religious affairs correspondent Robert Pigott said the Roman Catholic church denounced the regulations, claiming the rights of one group - gay people - were being placed above those of another - Christians.
Mike Judge from the Christian Institute said agencies were being forced to turn their back on their faith.
He told BBC Radio Five Live that so many agencies were abiding by the legislation showed "how aggressive" the law had been towards faith-based adoption agencies.
"I think it's iconic of a situation where you've got a clash between sexual orientation rights and religious rights where in almost every circumstance I've been aware of, religious rights have been seen to play second fiddle."
Cardinal Cormac Murphy O'Connor, head of the Catholic Church in England and Wales, warned the services of the 11 Catholic adoption agencies - which specialise in difficult to place children - would be "tragically lost to the country".
Catholic Caring Services - one of the agencies which has decided to comply with the regulations - has been disowned by the Bishop of Lancaster Patrick O'Donoghue, a fierce opponent of the new laws.
He has said the Preston-based charity would no longer be able to promote the Church's "moral teaching that a marital setting is better for children rather than being placed with a same-sex couple".
Another two of the agencies are seeking exemption from the law by having themselves registered as charities explicitly serving heterosexual and single people.
The position of the remaining three agencies is not known.