National Churchwatch is receiving a share of the £375,000 grant. The organisation provides advice on crime and security for churches.
Speaking to Premier News Hour, the organisation's founder, Nick Tolson said the funding was recongition from the government that Christian hate crimes do happen.
"[The government] were rather surprised that the majority faith in this country was actually suffering as much anit-religious crime as the minority faiths and it was something they hadn't really considered."
Other groups which will obtain part of the funding include The Sophie Lancaster Foundation - which fights hate crime against goths - and The True Vision which supports Sikh and Hindu communities that deal with hate crime.
The fourth group that will benefit from the funding is The Travellers Movement.
The announcement, which will be made by communities secretary Sajid Javid later today, comes after years of campaigning by groups to acknowledge that hate crime can happen to their communities.
Lord Bourne of Aberystwyth, minister for faith and integration, said the funding would help groups which find reporting and preventing hate crimes against them challenging.