The proposals would have restricted fishing and other human activities in some coastal areas.
Members of the Scottish fishing industry, coastal communities and even some MSPs had raised fierce objections to the marine conservation proposals.
Ms McAllan said: "We chose to consult as early and widely as possible on the principles of Highly Protected Marine Areas , with no pre-determined sites. It meant that all forms of fishing including recreational catch and release angling would be prohibited in selected sites. "Never have I experienced a policy that has received such overwhelming opposition from coastal communities, and Scotland's fishermen must now be at the heart of any proposals brought forward.
She said: "Ministers will now need to re-assure people that they are not simply intent on introducing the same policy by the back door."
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