The IPPC essentially requires industry to invest in more sustainable production techniques.
It deals with controls plants must have in place to reduce waste output and industrial emissions affecting the air and water, climate change, and the soil. Companies will have to spend additional sums to reduce the environmental impact of plant operations.
The directive, which gave existing plants until 31 October to comply with the rules, controls industrial emissions from a wide range of industrial and agricultural activities, including the processed foods sector, and poultry and pig farming.
New plant installations and those undergoing reconstruction have been obliged to comply with the directive since October 1999.
The IPPC system is based on a permit system for installations. The permits are handed out to individual plants by member states.
It is not sufficient that the competent authority simply issues a permit by 30 October 2007, the European Commission warned in a note this week.
"In order to achieve full compliance with the directive, the installation must also comply with the permit, which takes time because it often requires an upgrading of the installation," the Commission stated.
Most member states have decided to delegate their obligations under the directive to regional or local regulators.
All installations covered by the IPPC directive must now possess the permits to operate using a standard set of best available techniques (BATs) by the deadline.
The BAT documents outline a set of processing techniques agreed upon by the European Commission, governments, and industry and consumer associations.
The BATs may be used by plants to guide how they reduce pollutants resulting from manufacturing operations. In general, manufacturing plants will have to follow the techniques if they want permits to build or operate in the EU.
The food industry's BAT for food, drink and milk processing plants pinpoints water consumption, effluent discharges, energy use and waste generation as the most common environmental impacts across the food and drink sectors.
After 2007, regulators must update the permits for specific sectors whenever changes in BAT allow for new measures that significantly reduce emissions using cost-effective methods.
The permits do not prescribe the use of any techniques or specific technology, and they can take into account the technical characteristics of the installation concerned, its geographical location and the local environmental conditions.
In the determination of the BATs regulators have to take into account the reference documents on the BATs for specific sectors.
The reference documents (Brefs) are adopted by the European Commission based on an exchange of technical information on BAT between experts from industry, regulators, research institutes and non-governmental organisations.
The exchange of information is coordinated by the IPPC bureau in Seville (http://eippcb.jrc.es/), which sets up a technical working group for each Bref.
In the past the Confederation of the Food and Drink Ondustries of the EU (CIAA) has criticised the IPPC for "ambiguities" and called for revisions to better define the scope of activities and installations it covers.
To date, European food and drink industries have made significant investment in clean technologies and BATs, in order to conserve natural resources and minimise waste generation, the CIAA argues.
CIAA also called on the Commission not that make revisions that would lead to a change in approach, mainly towards benchmarking.
"Due to the high structural diversity of the European food, drink and milk sectors, including numerous sub-sectors, and due to large differences in locations, productions profiles and capacities of sites in each individual sub-sector, a very cautious approach must be taken towards benchmarking," the CIAA stated last year.