The Ministry has told the firm to clean up its emissions, after a survey found high quantities of dangerous chemicals in the air.
But Frutarom said it was " surprised " by the Ministry's decision and said they have invested in bringing the plant up to scratch.
Dan Tzafrir, global environmental manager, said: " We continue to work in collaboration with the Ministry and they are aware that in the last year alone we have invested about €0.5m to bring the best available technologies to our Haifa plant.
"We are confident that if such charges were to be brought to a court of law, any potential sanctions would not include closure of the plant."
Big Smoke
In June and September last year, the Ministry of Environmental Protection conducted surveys on the air quality in the Haifa Bay region.
It carried out tests at 20 sites in Haifa Bay and the immediate area.
Pollutants such as suspended dust, metals, hydrogen chloride, ammonia, hydrogen sulfide, marcaptans, volatile organic compounds, polyaromatics, dioxins and furans, were found in air samples.
Aldehydes and ketones, including formaldehyde, were also detected.
According to the Israeli newspaper Haaretz, the source of pollution has not been positively identified.
However, the ministry has prepared a list of factories including Frutarom that use these ingredients.
Letters from the director of the Haifa region of the Ministry of Environmental Protection, Robert Reuven, have been sent to suspect factories calling for them to bring about emissions reductions.
The Ministry of Environmental Protection will follow up on the implementation of these requirements.
The Haifa site is one of fifteen Frutarom production facilities around the world.
Both flavours and fine ingredient divisions of the Israeli firm operate from Haifa.
It produces oils, botanical extracts and aroma chemicals.
Other facilities are based in Switzerland, Germany, UK, US, China and Turkey.