The validity of Patent number: EP1646287B1 has been questioned in various research reports. How does one go about challenging the validity of the patent?
It seems to be too late. You may have already seen the report on this topic The Access and Benefit-Sharing Agreement on Teff Genetic Resources. It talks about the opposition proceeding that was held in the EPO in 2007 and the chance they had to appeal it. According to that report the opposers did not have enough knowledge of the patent system or ammunition in terms of data at the time. It is now too late to challenge this at the epo level and there are apparently plans for it to be challenged at the country level in Germany.
However the US counterpart US2006/0286240 has not issued and currently is under a "final" rejection. One of the grounds of rejection is that is trying to patent a product of nature.