"Our challenge is indeed to maintain the separation of risk assessment and risk management - indeed our independence," he told delegates yesterday at the International Union of Food Science & Technology's bi-annual conference, held this year in Nantes.
Koeter focused on providing an inside look at upcoming issues the agency is dealing with, such as health claims, antibiotics and nanotechnology.
Along the way he also described the various political pressures EFSA faces as it strives to maintain a firm line between its independent scientific research and the mire of EU politics.
That division is important to maintain the credibility of the advice the agency gives to European Commission, national regulators, industry and ultimately the public, he said.
After all regaining the public's trust after the BSE and dioxin scares was the raison d'être behind EFSA's formation in 2002.
The scares served to bring to the fore the ongoing differences in opinion and policy to food safety between the various regulatory agencies formed by member states.
"The BSE issue was hijacked by politicians," Koeter said. "It showed that newly established national agencies might handle issues differently. It showed that science and policy were often hard to distinguish and that food issues were used as non-tariff trade barriers. The same thing happened with dioxin."
EFSA was formed as an independent risk assessor of the food and feed chain, taking over the job of a committee that was directly part of the European Commission. The aim was to make scientific risk assessment independent, by separating the task from the management of those risks, which is the job of individual member states.
While EFSA has maintained that separation of science and state through its structure, political decisions have held it back.
For example the decision to locate EFSA in Parma, Italy was a political one, made as part of the bloc's policy to spread its institutions - and spending - outside of Brussels and Strasbourg.
However the decision has cost EFSA time and money, Koeter said. Parma does not have good travel connections with the rest of Europe. This has led to large amounts of time getting experts together so they can do their work.
Last year, EFSA spent €800,000 of its €31.5m budget just on ferrying people from other airports in Italy to Parma.
The move to Parma from Brussels last year also held up recruitment of more staff, as did EU approval of the agency's plans for more employees. EFSA remains at half of its projected staffing levels, but is now recruiting to come up to its full complement of 400 employees by the end of next year, Koeter said.
Still, the agency has managed to produce about 352 scientific opinions on food and feed safety issues from 2002 to the end of 2005. Koeter expects that number will reach 500 by the end of this year.
Hot decisions that had political repercussions included an assessment on the risks and benefits of wild fish compared to the farmed variety, a review of a controversial aspartame study, and an opinion on when measures have to be taken to protect unborn vertebrate animals from pain during scientific experiments.
Pressure comes from the European Commission, national legislators, regulatory agencies and industry to tone down or beef up results. Sometimes the pressure comes in the form of a push for a firm opinion on controversial subjects, when science is unable to yield a clear answer, Koeter said.
"We are sometimes under pressure from the Commission to make or give a decision in a certain way," he said. "However these are management issues."
The Commission and EFSA also sometimes clash on the shared area of communicating risk assessments produced by the agency. Koeter stands by EFSA's policy of informing the public directly on key issues and scientific findings.
The fear from the technocratic side is the public would misinterpret the science and turn away from a particular type of food, causing an economic loss for a member state or industry sector.
"It's a sensitive issue," he said. "We are sometimes told we are stepping over the boundary, but we always have to communicate to the public."
The declaration of interests by expert members of EFSA's assessment panels are also regularly challenged by what he describes as "critical parties".
EFSA's attempt to gather EU-wide statistics on zoonoses, diseases transmitted from animals to humans, also ran into a wall of national interests. Some members collected the statistics, others did not. Those that collected statistics sometimes downplayed some diseases while others did not.
EFSA published its first report on zoonoses last year, part of a bid to assess which ones to tackle and to set targets.
"It was like comparing apples and oranges," Koeter said. "Countries have different policies and attitudes to the statistics. Some claim to be Salmonella free. It depends on how a country wants to look at its foods."
EFSA has been working to set standards on the collection of such statistics to make reporting more uniform across the bloc. It is also looking to collect the statistics through other methods, such as by directly collecting information from doctors, for example.
Koeter believes that it is EFSA's committee structure and the use of a variety of outside experts that has kept its decisions free from political taint.
That structure will be put to the test in upcoming issues such as health claims, antibiotics and nanotechnology. All three issues arrive at the agency's doorstep in Parma, Italy laden with huge implications for industry.
This week the EU's Parliament is expected to vote in favour of a directive meant to harmonise health claims on food product labels across the bloc. The directive also hands the task of assessing nutritional features on which such claims can be made and the wording used.
EFSA is holding a conference on the issue with representatives from industry, consumer groups, scientists and legislators 8 to 10 November. About 200 people are scheduled to attend.
The last day's meeting will be webcast as part of the agency's policy to be as open as possible with the public.
EFSA also plans to hold another consultation on the issue of how to assess the risks involved with the use of nanotechnology to create novel foods, a task he describes as "extremely difficult".
Later this year the agency plans to publish its cumulative risk assessment of pesticides, and its opinion on the use of antibiotics, an issue that is the source of an ongoing trade dispute between the EU and the US.
The EU bans US beef because that countries uses antibiotics to speed up the rate of growth in cattle. It's an issue that has led the World Trade Organisation to decide against the EU ban.
EFSA's assessment of the playoff between the benefits of antibiotic use and the risks of promoting resistant strains of zoonoses is bound to throw some more scientific fuel to the political fire.