The ministry said it was acting on advice from the country's state earthquake protection authority (OASP), which inspected the Navagio beach on the Ionian island of Zakynthos on March 8.
The inspection found "extensive landslide risk due to erosion on the perimeter slopes", the ministry said, adding that the beach would be off-limits for this year's tourism season.
In 2018, seven people including a family of Czech tourists were injured in a landslide at Navagio beach, which lies beneath a cliff and is accessible only by boat.
A video shot by an onlooker showed a huge slab of rock sliding off the 200-metre (656-foot) cliff face above Navagio and crashing onto the sand, narrowly missing two people below.
At the time, the government said a 34-year-old Czech woman had been hospitalised with a fractured vertebra, while her husband and two children sustained light injuries.
Hundreds of people were on the beach at the time, including children.
Navagio, whose name means "shipwreck", is one of Greece's most popular beaches, taking its name from the remains of a cargo ship that was wrecked there nearly 40 years ago.
The site is also favoured by bungee jumpers and other extreme sports enthusiasts.
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