The body was discovered in the bottom of a deep trench at the site in Canary Wharf.
Police are investigating the incident but it is understood the victim was not a construction worker and the body lay undiscovered for a few days over the Christmas and New Year break.
Developer Canary Wharf Group said: “There has been a fatality at one of our construction sites, all our construction workers are safe and we are supporting the investigation being led by the emergency services.”
Canary Wharf Contractors are main contractor at the One Bank Street site which will be home to a 28-storey commercial scheme.