The finding comes in a skills survey of planners and ecologists by the Association for Local Government Ecologists (ALGE).
When considering a development, planners should first look for ways to avoid environmental harm, then mitigate for any adverse impacts, and only look at compensating for residual impacts as the final option.
Biodiversity offsetting, where planners require a developer to restore or recreate habitat elsewhere, should only be used as a last resort, the government has said.
But the survey found that the majority of local authority planners lack ecological qualifications and have little relevant training. Only around a third of planners have access to an in-house ecologist, ALGE found.
David Hill, chairman of biodiversity offset broker Environment Bank, said that if planners do not have ecological expertise they rely on developers' ecologists or local environmental groups who may be opposed to development.
But there was scope to pay for ecologists through the biodiversity offsetting system, he added.