Migrants will be asked to provide mouth swabs for DNA testing
Leading scientists have criticised as "naive" and scientifically flawed DNA tests for asylum seekers to establish where they come from.
The UK Border Agency "human provenance pilot project" is aimed at stopping people "swapping" nationality in the hope of remaining in the UK.
It is testing migrants to try to establish where they are from.
But scientists say it is not possible to tell what country a person comes from using the tests.
The pilot began earlier this month, targeting migrants from the Horn of Africa. Mouth swabs, hair and nail samples will be tested on a voluntary basis.
It is understood there is concern that some asylum seekers are pretending to be from countries like war-torn Somalia when making their asylum claims when in fact they are from neighbouring countries.
The Home Office said "nationality swapping is often used by fraudulent asylum seekers to help prevent their removal.
"That is why we are continuously looking at new and improved ways to ensure that we can ascertain the correct identity and nationality from every asylum seeker."
Professor Sir Alec Jeffreys of the University of Leicester pioneered human DNA fingerprinting. He described the pilot as "naive and scientifically flawed".
"It is bad science and could profoundly affect the lives of people, it's a shocker," he said.
"The Borders Agency is clearly making huge and unwarranted assumptions about population structure in Africa; the extensive research needed to determine population structure and the ability or otherwise of DNA to pinpoint ethnic origin in this region simply has not been done.
"Even if it did work, which I doubt, assigning a person to a population does not establish nationality - people move!", Prof Jeffreys said.
The magazine Science obtained Border Agency documents showing that, as well as DNA testing, hair and nail samples would be tested for isotopes, or different types of the same chemical element which relates to an individual's diet or their environment.
But Tamsin O'Connell, lecturer in bioarchaeology at the University of Cambridge, said using the samples that way would not enable the Border Agency to pinpoint a person's country of origin.
"It is very difficult to identify individuals to very specific locations using isotopes alone," she said.
"For example, you can't necessarily tell the difference between a Frenchman or a German. They can be used on a regional or continental level, but they don't relate to a political boundary."
The UK Border Agency maintains the scheme, which will last six months, will build up a clearer picture of where an asylum seeker comes from.
"This will enable the UK Border Agency to make further enquiries, including language analysis and face-to-face interviews, to indicate the possible origin of an individual and help successfully return them to their true country more quickly," a spokesperson said.