Canine behaviour assessments are commonly used in shelters to identify behaviour problems in dogs prior to adoption. The aim of this study was to evaluate whether kennel monitoring of dogs could identify early signs of behaviour problems, thereby facilitating early intervention and better management of dogs displaying behaviour problems. Kennel behaviour was monitored for dogs (n = 38) in their first five days in kennels at a shelter in Brisbane, Australia. This was compared to a formal assessment of exploratory, handling, play, run/freeze, and food guarding behaviour, as well as stranger and fake toddler interactions, and behaviour when the dog was alone, conducted five days after shelter admission. Kennel behaviours associated with fear, anxiety, and arousal in dogs were significantly correlated with the same behaviours in the formal assessment. Positional correlations were also evident. With respect to outcomes, dogs that displayed more whining, tense body posture, standing leaning forward, panting, ears forward, less barking, lowered body and balanced/relaxed body posture, standing still, and standing by the wall had increased odds of failing the behaviour assessment. Over the five days in the kennel, the frequency and duration of fear-related behaviours decreased, suggesting a reduction in arousal as the dog became accustomed to the shelter environment. The study demonstrates that monitoring kennel behaviour could detect early signs of behaviour problems.