The money comes from the Home Office's fund for schemes to tackle hate crime in communities and protect places of worship.
In addition nine community projects will benefit from over £300,000 for projects to help tackle specific types of hate crime.
Cash was also given to twelve mosques, one Hindu temple and one gurdwara.
The government announced the funding amid the increasing terror threat from Islamic State and other extremist Muslim groups.
Money can be used for CCTV, fences, gates, bollards, locks, alarms, lighting and new security doors. Churches were offered cash for the technology and to have it installed.
A spokesperson for the Church of England said it "welcomed today's announcement to fund schemes tackling hate crime in communities and protect places of worship."
They added: "Practical support to ensure places of worship, including churches, continue to be safe spaces helps our work in uniting communities, breaking down barriers and encouraging friendship."
Home Secretary Amber Rudd said: "This funding is the latest step in this government's mission to stamp out all types of hate crime, which has absolutely no place in a Britain that works for everyone.
"Alongside this, the security funding will help protect a cross-section of faiths from attack."
Communities Secretary Sajid Javid said: "This government is determined to tackle hate crime in all its forms.
"If we are truly to build a country that works for everyone, people of different faiths should be free to worship without fear of prejudice or attack."
