The introduction of fees would mean an additional cost for companies, which also have to pay for the scientific studies and investigations they must submit to the European Food Safety Authority (EFSA).
However the fees would help speed up the process of vetting ingredients, packaging and food contact materials for use in the bloc, according to consultants who drafted the consultation document.
EFSA was established two years ago as part of a package to co-ordinate food safety procedures throughout the bloc. It is meant to serve as an independent body providing science-based risk assessments relating to food and feed safety.
However in the consultation document the EFSA consultants argue that the regulator is underfunded and understaffed in relation to the work it is responsible for doing.
"EFSA is now at crossroads," the document states. "It must expand, develop, consolidate and build on its first success. Therefore, it must ensure that its structures, organisation, procedures and systems are fit for the challenges ahead."
The board notes that the 2005 budget was €36 million, below the €44 million originally promised and that introducing fees might ease the financial squeeze.
"The collection of fees by EFSA for opinions requested by legislation could ease the constraints but the idea needs some time to gain political acceptance and to be accepted by the interested stakeholders who are so far opposed," the consultants stated. "It is important that the relatively low level of current EFSA expenditures be not interpreted as 'EFSA does not need more'."
EFSA has issued relevant opinions with a reasonable cost in financial terms but with significant overtime work, a situation that is not sustainable, the board argues. A proper staffing level would be about 350 employees.
EFSA currently has about 70 permanent staff. Another 150 members make up the expert panels that issue scientific opinions.
"Timeliness of opinions can be improved, notably through more formalised negotiating procedures, as well as productivity thanks to recruitment and organisational measures," the consultants stated.
One way of getting more money and speeding up the process would be to charge fees for registering authorisations on ingredients such as genetically modified organisms, pesticides and feed additives.
The consultants noted that some people fear that this would change the nature of EFSA as a public institution. People might perceive EFSA as less independent after having authorised substances such as GMOs due to a potential conflict of interest.
Several of those interviewed in the drafting of the document believe that fees will not affect the independency of EFSA.
"But it will take some time to come to a political acceptance of a fee system, notably as the public might have less trust in EFSA," the consultants stated.
A fee system has several advantages. The fees would clarify the performance and resources of the two types of services offered by EFSA. One is services to the private sector, the other is to the European parliament and to member states.
The increase in funds from fees would help EFSA to issue opinions faster. About 17 per cent of opinions do not meet their legal deadline. Recently there has been a dramatic increase of deadlines not met, but this increase seems so far at least partly attributable to a change of reporting system, the consultants noted.
Extensions of deadlines and delays are related primarily to the understaffing of EFSA, as well as to internal organisation and coordination procedures.
Still with 76 per cent of the forecasted staff and 66 per cent of the forecasted budget, EFSA provides 80 per cent of the forecasted scientific opinions requested.
"This efficiency is however not sustainable," the consultants stated. "People are overstretched and, due to lack of time, they are not able to implement tools and procedures, to recruit, to train new colleagues and to ensure the continuity of the service. Incidents like burn outs of key persons might have severe impacts."
Another problem that EFSA needs to address is its location in Parma, Italy rather than in Brussels, the EU's headquarters.
EFSA estimates that the location in Parma is more expensive than Brussels has led to higher staff and travel expenses. More importantly the Parma location has led to a lengthier travel time for those attending meetings.
'The move to Parma is widely regarded as at least unfortunate and at worst disastrous for effectiveness of activity," the consultants noted. "Member states authorities and scientific experts alike point to problems of time and cost to travel - a one-day meeting now takes up three days and a plenary takes up the whole week."
The consultants suggest that an insistence on all meetings being held in Parma may be counter-productive.
The consultation document was issued by Bureau van Dijk Management Consultants and Arcadia International.
The deadline for comments is 28 February.