"[A plan to build the facility] does not exist at all," The Republic newspaper cited Hua as saying at a daily press briefing.
She added that the reports concerning building the environmental monitoring stations on Scarborough Shoal were mistaken.
According to the Foreign Ministry spokesperson, China placed great importance on the preservation of the South China Sea's ocean ecology, as well as on China-Philippines relations.
China has been in control of the shoal since 2012 after the standoff with Philippine vessels. Additionally, China denied the access of Philippine fishermen to the traditional fishing area, postponing access until a visit by Philippine President Rodrigo Duterte to China happened, which took place last year.
China, the Philippines, Brunei, Malaysia, Taiwan and Vietnam have long contested ownership of the areas in the South China Sea, which is recognized as one of the world's busiest sea lanes and is believed to hold vast oil and gas reserves.