The trees were over 100 years old said charity Trees for Cities, but would be felled and replaced by an 80m long Bomber Command memorial in 2012.
Sharon Johnson, chief executive of Trees for Cities said: "The ancient trees of Green Park are of immense value to the city.
"We appreciate the need for a memorial to World War II airmen but urge the proposers to consider alternative sites where the local environment will not suffer."
Trees for Cities swung into action this week after a funding of well over half the £3.5m cost was secured last week. Building work for Bomber Command Association is due to start in January.
Trees for Cities aims to create social cohesion through tree planting, community-led design, education and training initiatives in urban areas that need it most.