Sense Over Sectarianism, Nil By Mouth, the Scottish Book Trust and the Citizens Theatre are among the organisations receiving a slice of the money.
Housing associations, youth and football groups will also benefit.
A total of £2.3 million has been allocated for this year so far, with a further £700,000 still to be issued.
It follows funding of £9 million that has been granted to groups over the last three years.
Earlier this year, a study suggested a large majority of Scots believe sectarianism is still a problem for the country and that football is the biggest factor deemed to be contributing to the tension.
In the Scottish Social Attitudes Survey, the sport was the most commonly referred to factor for fuelling sectarianism, with 88% of people mentioning it and 55% saying it was the main contributor.
The finding emerged as 88% also said sectarianism is a problem for Scotland, although two-thirds (69%) believe it is only a problem in specific areas, such as Glasgow and the west.
Announcing the latest funding, Community Safety Minister Paul Wheelhouse said: “The Scottish Government is committed to tackling sectarianism. We have already invested £9 million over the last three years to support, among other things, community based efforts in dealing with sectarianism and this additional £3 million of funding will allow the issue to continue to be addressed at a local level.
“No one should have to face discrimination or prejudice in any form in 21st-century Scotland. It is never acceptable and it will not be tolerated.
“We welcome the fact that religiously aggravated offending is falling and is now at its lowest level in a decade - last year alone there was a 15% decrease. However we will continue to do all that we can to address the issue of sectarianism in Scotland.
“Communities are at the heart of our work to tackle sectarianism and that is why we have committed a further £3 million to support this agenda and to continue to work with, and in, local communities to tackle this issue in the most appropriate way.
“We are confident that these projects will help us to continue to reduce sectarian attitudes and behaviours and help to finally rid Scotland of the prejudices of the past.”