India, with the world’s largest cattle population, is a leading producer of milk, and claims to be self-sufficient for dairy production. However, such an important component for nutritional security has been reported to be adulterated by 68% by the national food safety agency. This study challenges the basic claim of self-sufficiency in terms of milk production and food security for milk and milk products. A novel model for studying milk safety is presented, which evaluates the prevailing conditions in the Andaman and Nicobar Islands (A&N), India. There are no comprehensive data nor studies available for this region. The assessment of the pillars of food security found that with the present population load, there is an annual deficit of 25673.7 MT of fluid milk in the A&N Islands. The study found that the average herd size is 1.9, with about 26.9% of the animals rearing desi (non-descriptive) cattle, characterized by low production levels of 3.95 L/day and with gene frequency of 16.48% for the A1 allele. None of the milk samples were found to be positive for antibiotic (tetracycline and aminoglycoside) residues. However, 4% of the milk samples were found to be positive for the aflatoxin residues above the permitted MRL. The KAP study shows that awareness regarding clean milk production, antimicrobial residues, withdrawal timings, aflatoxins, etc. is poor/highly limited among the farmers of the region. The output may act as a referral study and a template for future studies for the assessment of product-specific food security. Our findings highlight the limitations of the present approach and the need for additional data, using a wider range of research techniques for assessing dairy. Whilst not definitive, it aims to highlight those factors which are considered crucial to an understanding of contemporary milk safety controls.