Long Bay is patrolled by surf lifesavers between noon and 7pm. The other two beaches are unpatrolled.
The alerts come eight days after Hamilton woman Kaelah Marlow, 19, died from injuries she received in a shark attack at Waihī Beach.
Two days later Pāuanui Beach was closed for several hours after surf lifesavers spotted three sharks.
Clinton Duffy, a marine scientist at the Department of Conservation, told the Herald this month many people had the mistaken perception that sharks were uncommon in New Zealand.
"There are actually quite a lot of sharks in New Zealand waters, and large sharks are reasonably common in-shore.
"They can even be very abundant in some places in-shore over the summer."
While attacks were uncommon - he counted just 14 fatal attacks since 1840, including the death of Adam Strange while swimming at Auckland's Muriwai Beach in 2013 - people should always swim between the flags, and never alone at a non-patrolled beach.
Swimming at night, and where people are or have been fishing, should also be avoided.
Large concentrations of fish in the water or the presence of dolphins could also indicate the presence of sharks.
"For the most part, sharks are completely uninterested in humans, I've seen them myself swimming past people ... taking no interest at all," he said.
