A high tide or extreme wind conditions probably caused the animals to be washed off Seal Island on Thursday night and officials say it is not a particularly unusual phenomenon.
Hundreds of dead seals are scattered around the peninsula from Strandfontein as far as Kommetjie.
Those passing by say the mammals have been laying there for hours.
An onlooker who drives past Muizenberg Beach everyday says he spotted the seals on the shore at 7am.
According to disaster management's Johannes Solomons-Johannes, there are more 100 dead seals which must still be removed between Strandfontein and Monwabisi Beach.
Meanwhile, the Society for the Prevention of Cruelty to Animals (SPCA) says it is not that unusual for dead seals to wash ashore in Cape Town at this time of year.
However, it is surprised by the sheer number of carcasses which washed up on the False Bay coastline.
SPCA spokesperson Brett Glasby says the City of Cape Town is conducting a clean-up.
"These high winds and high seas washed over the Seal Island and seem to wash off any of the young seals that can't swim and any seals that have died on the island," he says.
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