Arrange racks in the upper and lower thirds of the oven and preheat to 350 degrees F (175 degrees C). Line 2 large baking sheets with parchment paper or nonstick foil.
Stir coconut, flour, and salt together in a large bowl. Stir in sweetened condensed milk and vanilla extract until well blended. Use a medium cookie scoop to scoop and drop 2-inch balls of dough onto the prepared sheets. Using your thumb, make an indentation in each dough ball.
Bake in the preheated oven until coconut is toasted and bottoms are golden, 15 to 17 minutes, rotating pans halfway through. If cookies puff, re-press centers with the rounded side of a measuring teaspoon. Cool on the sheets for 5 minutes. Transfer to a wire rack; cool completely.
Spoon a scant teaspoon of caramel topping into each indentation. Sprinkle each with several flakes of sea salt.