Religious leaders in Kenya are set to oppose a High Court ruling that gay rights activists can officially register their organisations.

On Monday, the High Court ordered the NGOs Coordination Board to recognise and register a 2013 petition by the National Gay and Lesbian Human Rights Commission. The organisation had previously been rejected five times on moral and religious grounds, but the court has now ruled for the protection of the rights of "every person" to form or join associations, including minority groups.

Same-sex acts are criminalised under Kenyan law, and the Kenya Human Rights Commission reported in 2011 that "LGBTI persons are routinely harassed by the police, held in remand houses beyond the constitutional period without charges being preferred against them, and presented in court on trumped-up charges." Clergy regularly preach against homosexuality, and some have called for more severe punishments – though anti-gay laws in the country are already among the harshest globally.

Archbishop Eliud Wabukala, head of the Anglican Church in Kenya, said the Church would oppose the new legislation, which he branded "naïve". Wabukala is also the chairman of the Gafcon primates' council, a group of conservative Anglican bishops and leaders.

"The judgement was made on very narrow considerations and it is not only against Christianity but also against the Muslim teachings and traditions," he said on Wednesday.

"The church supports a family unit and the society at large. Families can only be formed through the right family unit. Any law that goes against the family values is naïve and should not be allowed in any country."

Christian groups have also begun contesting the new ruling. The Kenya Christian Professionals Forum (KCPF) said it was "aggrieved" by the Court's decision.

"To allow registration of advocacy group advocating for those who are practicing the sexual acts against the order of nature raises concern," the group said in a Facebook post, warning that the freedoms granted "are against the letter and spirit of our Penal code and their exercise threaten to restrict the freedoms of others."

KCPF said it will appeal against the judgement "on behalf of the public interest".

However, pro-gay activists in Kenya have unsurprisingly welcomed the legislation, including some religious leaders. Pastor John Makokha of Riruta Hope Community Church in Nairobi has been working to promote LGBT rights for years, despite opposition. He has previously expressed a desire to end "religious homophobia".

"Gays and lesbians are children of God and created in his image," Makokha has said. "They should be accepted and affirmed as such. They deserve a place to worship and serve God."

He told the Huffington Post that he was pleased with the latest developments, but is concerned at the pushback likely to come from many in the religious community.

"I see religious groups going full-length to challenge it using their doctrines. We have to ensure that [the right of association] does not remain guaranteed in the constitution but cannot be practiced on the ground."