The new scheme is being designed to help protect such venues from hate crime and be open to all places of worship in Scotland.
Justice Secretary Humza Yousaf and Communities Secretary Aileen Campbell announced the new scheme during a visit to Garnethill Synagogue in Glasgow.
Mr Yousaf said: “We recently committed to exploring what we could do to ensure safety and security for our faith communities at their places of worship, including developing a security funding scheme.
“I hope that this scheme will provide reassurance to all faith communities and their places of worship that hate crime and prejudice will not be tolerated.”
The fund will launch later this year with religious groups to be consulted over the coming months to help develop it.
Ms Campbell said: “We are committed to ensuring that our communities in Scotland feel free to practise their religion in a place where they feel safe.
“No-one should fear being attacked because of their faith and particularly in their place of worship.
“We are determined that all places of worship should be places of peace and sanctuary and that our faith communities feel safe and secure when they visit them.”