Highlands and Islands Enterprise (HIE) has approved the new package of funding.
It will run the trial programme in conjunction with the Scottish Aquaculture Innovation Centre.
The project has been set up to help small businesses to commercialise new innovative products for the fish farming industry.
Public agency HIE said the initiative could increase the industry's turnover in the Highlands and Islands by about £8m and create up to 50 jobs.
Rural Economy Secretary Fergus Ewing said: "Scotland's aquaculture industry is a real pillar of our rural economy, particularly for the Highlands and Islands, and this government is committed to working with partners across the sector to support continued sustainable growth.
"Maximising the opportunities that innovation can bring will be central in delivering the industry's vision for the future of aquaculture.
"That is why it's pleasing to see this collaborative programme come to fruition, which will provide a boost for the sector and support job creation."
A £1m initiative to boost innovation in aquaculture in the Highlands and Islands has been given the go-ahead.