The scheme will fund security measures including CCTV, alarms and improved locks at places of worship vulnerable to attack.
Prime Minister Theresa May said: "We are a country of many faiths, and as I said following last year's appalling terror attack in Finsbury Park, an attack on one community is an attack on all of us.
"Freedom of worship, respect and tolerance for those of different faiths is fundamental to our values and I am determined to stamp out extremism and hate crime wherever it occurs."
Successful applicants in England and Wales will receive up to £56,000 towards improved security to counter the threat at their premises.
Previous funding has been awarded when places of worship have been subjected to offensive graffiti, the defacing of religious symbols or attacks on worshippers.
Bidders will need to provide evidence they are vulnerable to hate crime or have been subject to a hate crime in the last two years.
The Places of Worship Security Funding scheme, which launched in 2016 and is worth £2.4 million in total, has helped 89 churches, mosques, temples and gurdwaras to install protective measures to deter attackers.
Synagogues are covered under a separate scheme administered by the Community Security Trust.
Baroness Williams, the minister for countering extremism, said: "Communities being able to worship their religion free from intimidation, violence or abusive behaviour is a vital principle at the heart of the values we share in this country.
"This scheme has already helped many places of worship bolster their security and we encourage those who have suffered from or fear hate crime attacks to apply."
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