The stand would include 64 residential flats, and it is this that saw the council's planning committee reject the plans.
Hearn, who plans to appeal, blasted: "At a time when councils across the country are clamouring to help their local clubs, we are dismayed that the London borough of Waltham Forest have taken such a short-sighted decision.
"With the Olympic Games looming in the area in 2012 it is surprising the local council lack the vision to embrace this regeneration and landmark development in the borough.
"The future of the club within the borough is under threat if we are unable to finish our stadium."
Last week the London side secured the signing of Birmingham City winger Peter Till on loan.
Till spent the early part of last season on loan at Glanford Park.