A Basel-based pressure group has called for the suspension of funding for a national research study, which aims to examine unborn babies and children.
Criticism of the project has also come from a member of a Swiss government ethics advisory committee.
However, the National Science Foundation has defended its decision to support the project, saying it is too early to judge the research methods.
Citing legal and ethical grounds, the Basel Campaign Against Gene Technology has harshly criticised the groundbreaking study.
Basel university professor and team leader of the study, Jürgen Margraf, has strongly rejected the claims of the Basel group.
"We're not a gene technology project, this is a project about human development, personality and mental health. One component of the project is genetic, looking at how genetics interact with the environment."
The project, Swiss Etiological Study of Adjustment and Mental Health, is to recruit and examine a population sample of 3,000 children from early pregnancy to 20 years of age, along with their parents and grandparents.
The aim of the multi-disciplinary study is to understand "the pre-disease pathways leading to the development of mental disorders and maladjustment". The government approved funding last March.
Pascale Steck, director of the Basel campaign, says research into the genetic make-up of the children will form a central part of the study.
This is the first time Swiss children have been included in such a project with a genetic element," Steck told swissinfo. "Children cannot give permission for their DNA to be examined, recorded and researched."
Margraf told swissinfo that the issue of permssion was no different in this case to any research involving children.
"One has to acknowledge that parents normally make decisions for their children that can be far-reaching. This study will comply with the ethical standards that apply to any type of research involving children."
In the study, research groups from the various psychological, social, biological and health disciplines will work together on the large, representative population sample.
Steck also raised the issue of data protection. "We don’t know who will have access to these data in the future and that is worrying. It is very important for this kind of data to be well protected."
Reservations have also come from Carola Meier-Seethaler, a member of the Swiss National Advisory Commission on Biomedical Ethics.
"What I have read about the project makes me sceptical. I find it dangerous to take a three-month-old foetus as a test person until it is 20 years old," she commented.
Meier-Seethaler was also concerned that young children were not in a position to consent to being test people.
A spokesman for the Swiss National Science Foundation, which has allocated SFr10.2 million ($8.1 million) to the project over the next four years, told swissinfo that the criticism was premature.
"It is too early to speak about the ethical side of the project because we have not yet reached the stage of examining and approving the individual research components.
"All the ethical questions will be examined in detail before the project begins. We are obliged to do that and we will do that."
The study was one of six scientific projects selected by an international panel of experts and approved for Federal funding in March.
The aim of the project is to understand how mental health develops and how the mind adjusts to the social, psychological and biological environments in which the participants live.
Beginning with pregnancy and including the entire "risk period" for the development of most mental disorders, the sample of 3,000 will be tracked and analysed in different ways.
The project, which is being coordinated from Basel University, hopes to identify optimal intervention points for public policy, healthcare and personal well-being.
swissinfo, Clare O’Dea
The Swiss National Science Foundation has granted funding to a 20-year study of adjustment and mental health.
The project will examine genetic, environmental, psychological, social and biological risk factors, seeking to understand the root causes of mental illness.
An anti-gene technology group has called for Federal funding for the project to be suspended.
The group objects to researchers studying the genetic make-up of 3,000 children from the 12th week of pregnancy to adulthood.