Mr Lochhead's comments come as talks are due to begin in Brussels on the fund which is to replace the European Fisheries Fund (EFF) from 2014.
He said: "The package of measures agreed to in the ambitious reform of the Common Fisheries Policy (CFP), which we hope will lead to sustainable fishing with discards being tackled and fisheries management decisions being taken locally, was based on the understanding that the new EMFF will fully fund these plans.
"With more than £155 million of investment delivered through grants to date, the current EFF is delivering a diverse range of support for fishermen, processors, fishing communities and aquaculture sector."
Scottish fishing zone is 61% of the UK fishing zone and is Europe's seventh largest. Scotland has 17% of the EU acquaculture.