"There are reservations about the project concerning several aspects: marine life, scientific research, impact area, assessment of the impact on different species," Rojas said.
"Based on this, the committee of ministers made a unanimous decision to agree with 12 claims, the port and mining project of Dominga received a negative assessment."
The project, which has been developed by Chile's Andes Iron since 2013, includes a mine, a plant, a waste storage, a shipping terminal and a system of underground pipelines.
The Dominga project was planned to be located some 500 kilometers (310 miles) north of Chile's capital of Santiago near ecological reserves, drawing criticism due to its potential negative impact on environmentally sensitive areas.
The company, in turn, rejected all claims, saying that the project complied with the country's environmental standards, and stated it would turn to the courts to overrule the committee's decision.
According to Chile's former environment minister, Marcelo Mena, the legal battle around the decision could take up to two years.