The largest southern hemisphere humpback whale Megaptera novaeangliae stock (El) uses the east coast of Australia as a migratory corridor to travel between their high-latitude feeding grounds in the Southern Ocean and low-latitude breeding grounds in northeast Queensland and the south-west Pacific Ocean. The population is recovering at close to the maximum rate of growth (rm), and the increasing abundance of whales passing within sight of land has facilitated the development of a growing land- and vessel-based whale watching industry. We observed the behaviour of 156 individual pods of humpback whales passing Sydney, New South Wales, during their 2006 and 2007 northern migration and monitored vessel-whale interactions with respect to the Australian National Guidelines for Whale and Dolphin Watching 2005. We applied generalised linear mixed models with random effects to compute the odds of changing to the current behaviour state. We found that in the presence of vessels, whales were more likely to remain on the surface breathing or to cease surface breathing and switch to generally short, shallow diving than was the case when no vessels were present. Northerly migrating whales off Sydney were more likely to remain on the surface breathing in the presence of vessels, rather than taking some form of vertical avoidance (deep, long dives) as reported elsewhere. Given the high rate of population increase of stock El and the low level of behavioural changes seen, it appears that for this population at least, adult humpback whales migrating to their breeding grounds are relatively robust to disturbance by whale watching.