The SSPCA were called to the scene by a member of the public following concern for the animal.
The organisation have confirmed that the seal will be cared for by them but should be able to make a return to the wild.
Scottish SPCA senior animal rescue officer, Sarah Auldsmith, said, “We were called to a report of a young seal at Port Seton Harbour at around 8am on Friday 3 December.
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“The seal was underweight so has been taken to our National Wildlife Rescue Centre at Fishcross so our team can help the animal put on enough weight to survive independently.
“Thankfully, other than being a bit thin, the seal appears to be in good health so hopefully will not have to stay with us too long before being released back in to the wild.
“Seals often haul out on to land to rest so this is not cause for concern in itself. However, if anyone spots a seal which has been in the same position for a number of hours, especially if it has a white coat or is visibly sick or injured, they should call our animal helpline on 03000 999 999.”
Earlier this week, hundreds of seal pups were killed as Storm Arwen lashed the Scottish coast.
The National Trust for Scotland estimated that 800 seals are thought to have perished at St Abbs Head reserve near Eyemouth