UPDATED POST- 10 January 2014: Changes Paragraph Reference for New AR 600-9 2013
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AR 600-9 is very clear on this issue. Please see the extract below:
Extract AR 600-9
3–4. Weigh-in and body fat assessment
c.Routine weigh-ins will be accomplished at the unit level. Percent body fat assessments will be accomplished bycompany or similar level commanders (or their designee) in accordance with standard methods prescribed in appendixB. Soldiers will be measured by trained individuals of the same gender. If a trained individual of the same gender isnot available to conduct the measurements, a female Soldier will be present when a male measures a female, and a male Soldier will be present when a female measures a male. IRR members on annual training, ADT, and special ADTwill have a weigh-in and body fat assessment (if required) by the unit to which they are attached.