The Cabinet Secretary has raised the issue with the UK Government on a number of occasions - including highlighting the fact that Scottish levy money has been used to promote frozen Norwegian fish in the UK market.
The Scottish Government will now push for maximum autonomy within the current system to ensure the levy can be better used to promote the range of and quality of Scottish seafood at home and abroad.
Mr Lochhead said: "“The UK Government’s continued refusal to devolve the seafood levy is illogical, damaging and a missed opportunity. Quite clearly, decisions on spending levy raised in Scotland should be taken in Scotland in the interests of Scotland’s seafood sector.
“If Scotland were allowed to take these investment decisions it would enable us to properly support our industry by promoting the quality and excellence of Scottish seafood products in markets at home and across the world. We currently have the absurd situation where Scots levy money has been used to promote frozen fish from Norway in the UK but can't be used to promote our own seafood as ‘Scottish’.
“Scotland’s seafood sector is primarily based on landing and processing fresh fish through a range of small and medium-sized enterprises which maximise the benefits of Scottish provenance and supply top quality products to the consumer.
"That’s where we could focus our investment if we had a Scottish levy. It’s a world away from the large scale importation of foreign-caught frozen fish, which dominates the sector in so much of the rest of the UK.
“That’s why I am extremely unhappy at the UK Government’s decision and why I am left with the only option of pushing for maximum autonomy for Scotland within the current arrangements.
"Unfortunately that’s very much the second best option for our industry but administrative reforms can at least give Scotland the key role in deciding how the Scottish share of the levy should be spent. That will let us promote the Scottish seafood sector in the best possible way – a move that is clearly supported by many in the Scottish industry.”