The new protected areas -- in the Ionian Sea and in the Southern Cyclades in the Aegean Sea -- would be "among the largest marine protected areas in the entire Mediterranean", he said in a video message in English.
The prime minister said that the "hugely damaging practice of bottom trawling" by commercial fishing boats would be banned within the new marine reserves and in all Greece's marine protected areas by 2030, making it the first country in Europe to take such a significant step in preservation.
Fishing is generally allowed in protected marine areas worldwide, even by trawlers which scrape the seabed with a huge funnel-shaped net, to devastating effect.
Mitsotakis said that he had "made a promise to honour (Greece's) unique marine heritage" at last month's UN Oceans Conference in southern France, "and to protect it for generations to come".
"Today I am delivering on that promise with the establishment of two new marine national parks... because when we protect our ocean, we protect our own future."
Greece is located in the eastern Mediterranean and has around 13,600 kilometres (8,450 miles) of coastline and thousands of islands.
Greece, Brazil and Spain all used the UN conference in Nice, to announce new protected marine reserves and measures to ban bottom trawling, in order to better protect marine wildlife.
Mitsotakis said that the size of the new Greek marine reserves "will enable us to achieve the goal of protecting 30 percent of our territorial waters by 2030".
He said that the government would work with "local communities, local fishermen, scientists (and) global partners (to) make these parks examples of what is possible".
- The oceans are 'life itself' -
In May, Athens banned bottom trawling in the waters of the Fournoi Korseon island chain in the Aegean to protect recently discovered coral reefs that are exceptionally rich in marine wildlife.
Neighbouring Turkey, whose western coast is close to the Aegean islands, responded to Monday's announcement by criticising such "unilateral action".
"International maritime law encourages cooperation between the coastal states of these seas, including on environmental issues," the foreign ministry in Ankara said.
It said that Turkey was willing to cooperate with Greece and would soon announce its own plans to protect maritime areas.
Greece and Turkey, both members of NATO, have historical disputes over maritime boundaries in the Aegean Sea.
They signed an agreement in 2023 aimed at easing tensions.
Mitsotakis said that "Ocean", a new documentary by British natural history broadcaster Sir David Attenborough, had inspired Greece to accelerate efforts to protect life below the waves.
"Ocean", which features spectacular footage of undersea habitats and marine life, emphasises the importance of healthy seas for tackling climate change and the current sweeping loss of wild species across the planet.
Mitsotakis said "Ocean" showed that the sea was "not just beautiful scenery".
"It is life itself. Delicate. Powerful. And under threat."
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