Alun Davies told AMs they had received 7,000 responses to a consultation containing "strongly held" views.
He said he would now look at the 125 existing marine protected areas to see if further improvements could be made.
The Marine Conservation Society (MCS) described it as an "embarrassing U-turn" for the Welsh government, and has called for better protection of seas.
Creating the zones would mean a ban on fishing and anchoring in some areas and had brought opposition.
The Welsh Fishermen's Association said previously that existing conservation networks for Welsh waters are adequate.
The Welsh government proposed the zones last year with the backing of the Countryside Council of Wales and the Marine Conservation Society.
The minister for natural resources said the decision had been made after the thousands of responses to the consultation brought "divergent and strongly held views".
Mr Davies said to "avoid any continuing uncertainty over the options presented in the 2012 consultation, I am also withdrawing all the proposed sites".
His comments come after the findings were published of a task and finish team which reviewed the feedback.
Now, he will concentrate on the existing 125 Marine Protected Areas (MPAs) that cover 36% of Welsh seas to see if any changes can be made rather than creating additional zones.
"We are now in a stronger position to assess our current contribution to the network's ecological coherence," he said.
"I have, therefore, commissioned an assessment of our current MPAs to identify if there are any gaps and what the options might be to fill those gaps.
"If any measures are required, I believe they should be simple, proportionate and fit for purpose."
Dr Peter Richardson, biodiversity programme manager for MCS, said the Welsh government "spent an awful lot of time and money and encouraged other people to put effort into this consultation response".
He said: "70% of the consultation responses were in favour of designating these sites and yet today the minister has announced he's scrapping the whole thing... bit of an embarrassing U-turn for the government I think."
He added: "I think there are plenty of people in the fishing industry... that understand that in order to get the best yields from the marine habitats on which they depend, they have to be managed properly."
Controversial plans for 10 marine conservation zones have been withdrawn by a Welsh government minister.