The Baptist Church, the Church of Scotland, the Methodist Church and the United Reformed Church have all expressed their opposition at the so-called "two-child limit".
Rachel Lampard, Vice-President of the Methodist Conference, told Premier: "We're going to see a rise in child poverty of around one million by the end of this decade; that's why we're so opposed to these changes.
"Child poverty obviously means a worse upbringing for children but it also has longer-term implications."
From Thursday, babies born to families with at least two other children will no longer be granted Universal Credit, in a move the government says is trying to encourage more people into work.
A Department for Work and Pensions spokesperson said: "This policy helps ensure that parents on benefits have to make the same choices as those supporting themselves solely through work.
"Current claimants won't see any reduction in their benefits as a result of this policy, and we will continue to pay Child Benefit for all children in a household."
The two-child limit will also be applied retrospectively from November 2018.
Rachel Lampard added: "Our concern with this is that the two-child rule basically takes a knife to the social security safety net and we fear that hundreds of thousands of the UK's most vulnerable children are going to fall through the gaps created."