The cash - Scotland's allocation from the European Fisheries Fund (EFF) for 2008 - will be fast-tracked, meaning it can be accessed up to the end of March but bids must be received by the end of the year.
In the Scottish Parliament, Environment Minister Michael Russell praised the aquaculture sector for a reduction in incidents of escaped fish in 2007 and called on the industry to look at re-siting some farms to more appropriate areas.
Mr Russell said: "The Scottish aquaculture sector is absolutely vital to our economic growth. With farmed Scottish salmon in particular recognised as a global brand, the sector is worth around £400 million every year.
"In the current economic climate it is absolutely vital that our fish producers take advantage of every resource available to them and that includes the European Fisheries Fund (EFF).
"There is up to £3 million available for suitable projects that can start quickly and deliver immediate benefits, and I would urge the industry to think about how they could reap its benefits.
"A few months back in Skye, I launched a consultation on the Strategic Framework for Scottish Aquaculture, a five point plan to ensure a sustainable and profitable industry for the future.
"A 20 per cent reduction in farmed fish escape events between 2006 and 2007, and early figures for 2008 suggest that the industry is on course for a significant improvement on the number of escaped fish.
"This is a good indicator that we are making progress on some of the Framework's points, ahead of its final publication in the spring, alongside new regulations to ensure that all fish farms adhere to the highest possible standards.
"Today is also an excellent opportunity to publish, for the first time, a map of marine fish farm sites around Scotland. This will help illustrate the value of and extent to which our rural and coastal communities rely upon aquaculture.
"With that in mind I would challenge the farmers to use the money available to tap unused sites and support efforts to achieve farm sites in the best places for business and the environment.
"The need for fish farms to be a good neighbour is paramount as we work to ensure a bright and prosperous future for aquaculture in Scotland."
Eligible projects might include:
- the development and delivery of professional, safety and specialist skills training
- improved management, sustainable exploitation of resources, improved hygiene standards and minimisation of environmental impacts
- pilot projects in partnership with scientific or technical bodies
- long term profitability in global and local markets to the benefit of producers and consumers
- development of new markets and promotional campaigns including on quality, value enhancement and environmental credentials for fisheries and aquaculture products
- campaigns to improve the image of fisheries and aquaculture products and image of the fisheries sector implementation of market surveys