There is Pelekita Cave following the cost to the north from Kato Zakros. Sometimes it is told "Sykias Spilios" because of the tree at the entry of the cave. It takes between 1 and 1 1/2 hours walking for the 6 km. The same back.
Pelekita Cave is located at the small bay of Karoumbi. There are signs of neolithic habitation. As well there was found also the qarry from where the ancients took the stones to built their Palace.
See some pictures at Interkriti (follow the link "The Cave"): the cave, stalagmites and stalactites
There is an interesting report in *.pdf-format from Kreta Umweltforum. It is in German, but pictures do speak alone: 142-06 - Pelekita-Hoehle.
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Think about taking a torch with you to take a look into the cave. Then you can see the impressive stalagmites and stalactites. It measures 310 m and has 4.500 qm.
It may be a hard way to walk in the hot summer, there is no place to rest in shadow. Please care for water to drink on the very lonely way. It sometimes is heavy to walk because of the stones. Do not walk with bad shoes. Take care for children. At some places the way is not secured and it goes 30 m deep down to the sea.
Take care inside the cave. The first part is easy to enter. Then it could be very dangerous to go on. Go never into the cave alone. Do not destroy anything. Do not take out anything. Please do not leave any rubbish.