The apparent association between high dose B12 supplementation (not B12 in food) and increased risk for lung cancer is very weak. Firstly, the authors say that the association is not present is non-smokers, nor former or recent smokers, and not present in women. So we are left with an association in men who have smoked for a long time and continue to do so.
One common misunderstanding, with makes this study very weak, is that the statistics, while derived from a seemingly large survey of 77,000 people only relates to 139 people.
Out of these the only significant apparent increased risk, in relation to vitamin B6, was derived from 12 people who used to take more than 20mg of vitamin B6 who appeared to have double the chance of having got lung cancer compared to those who didn’t supplement. Those who continued to take B6 had a fraction of this risk.
In relation to vitamin B12 we are talking about only 18 men who have smoked for some time and continue to do so, and used to take vitamin B12 above 55mcg a day who were found to have more than double the risk of having lung cancer. However, those who continued to take B12 at or above this dose didn't have a significant increased risk.
So, if one can legitimately get concerned of the basis of a study of a couple of dozen men the concern would only be of relevance to men who have smoked for some time and continue to smoke, and used to take high doses of B6 or B12, and no longer do.
Other studies have found the opposite to be true. A study in 2016 found that the risk of developing lung cancer was reduced by half (50%) in people with high levels of B6, and by two thirds (66%) by those with high intakes of folic acid as well. This was based on a survey of 385,000 people in Europe and was published in the Journal of the American Medical Association.
If any concern is justified, which requires a stretch of the imagination, the take home message could just as legitimately be “if you’re a man and a long-term smoker taking high dose B6 or B12 supplements - don't stop!” rather than the over-exaggerated fear-inducing headlines that sell papers. Or, alternatively, stop smoking.