Section 4 of PD 1586 provides that no person, partnership or corporation shall undertake or operate any such declared environmentally critical project or area without first securing an Environmental Compliance Certificate (ECC). Full implementation transpired after the issuance of Presidential Proclamation 2146 in 1981 where Environmentally Critical Projects (ECPs) and Environmentally Critical Areas (ECAs) were defined. Hence, ECPs and projects within ECAs established from 1982 onwards are required to secure ECC.

ECC applications and issuance was initially with the National Environmental Protection Council (NEPC) under the Ministry of Human Settlements. With the creation of the Regional DENR Offices and under DENR Administrative Order 21 (1992), processing of ECC applications for Non-Environmentally Critical Projects in Environmentally Critical Areas was devolved and the Regional Executive Director of the DENR was given the authority to grant or deny ECCs to Non ECPs in ECAs. In November 2002, the Office of the President through Administrative Order 42 authorized the EMB Regional Directors to issue ECCs.