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."

Stable-mates Lewis and Harris are named after neighbouring islands in the Western Isles.
Harris, whose name was chosen by the public in an online vote last week, has been joined this week at Police Scotland's mounted unit by Lewis.
The force described Lewis as "lovely and quiet" and also its smallest horse at about 16.2 hands high.

Sylvia Blackburn, 72, suffered serious head injuries outside Bedford Road Lower School, Kempston, on 19 December 2014.
Luton Crown Court heard Brian Wright, 55, of Kempston, said he was unable to see at the point of impact.
He denies causing serious injury by dangerous driving.
Prosecutor Sally Mealing-McLeod said Mrs Blackburn, a lollipop lady for 20 years, had been on duty in Bedford Road as pupils were leaving school on the last day of term.
She was wearing a long-sleeved high-visibility orange and yellow coat which had reflective strips and "school crossing patrol" written on the back.
When the traffic lights turned red, she stepped out to escort a woman and her six-year-old daughter across the road.
Traffic travelling in the opposite direction stopped, but Mr Wright's VW Golf failed to stop and hit her at 14mph, the jury heard.
Witnesses described Mrs Blackburn's head hitting the screen pillar of the windscreen before she struck the wing mirror and then the road.
The married mother of three was airlifted to Addenbrooke's Hospital in Cambridge.
She was later transferred to Bedford Hospital and is now at a residential care home for people with an acquired brain injury.
Mr Wright, of The Dell, declined to comment in police interview but in a statement said he was blinded by the setting sun and lowered his visor but was unable to see when the collision happened.
The court heard the sun was 10 minutes from setting and could have been shining into Mr Wright's eyes.
Ms Mealing-McLeod told the jury that if his vision had been affected he should have stopped.
The trial continues.
Controversial plans for 10 marine conservation zones have been withdrawn by a Welsh government minister.
[NEXT_CONCEPT]
Scotland's newest police horses have been named after two of the country's most famous islands.
[NEXT_CONCEPT]
A driver "blinded" by the sun drove through a red light at a pedestrian crossing and knocked down a lollipop lady, a jury has heard.