Mr Duffy described mako sharks as aggressive and said they had been known to attack humans.
The growing numbers of kahawai and small fish in the area were also attracting mako and other shark species, Mr Duffy said.
Meanwhile, the recovery team will survey Whale Island and a helicopter will today fly to Motiti Island to inspect beaches for container debris, asays Maritime New Zealand.
During the weekend, 17 containers were taken off the Rena, taking the total removed by salvors to 227.
When the ship struck the reef off the coast of Tauranga on October 5, there were 1368 containers on board.
A container with meat products inside fell off the Rena on Sunday and was recovered, taking the total number of containers washed overboard from the ship to 89.
Braemar Howells is processing more than 200 containers that have been brought ashore.
"Dive inspections have been conducted on a regular basis and buckling damage adjacent to the No 6 hold on the starboard side continues to develop," Maritime New Zealand said.
"This is consistent with previous inspections following periods of bad weather and this will continue to be monitored."
A narrow sheen of oil was also visible off the bow of the Rena to the northwest.
On Sunday, 23 little blue penguins that were rescued from Motiti Island were released after being cared for at the Te Maunga oiled wildlife facility, leaving 43 little blue penguins and one dotterel still in the centre's care.
Two clean-up teams are operating at Mt Maunganui, with one undertaking warm-water washing and the other scraping rocks. A third team is working in Kulim Park.
Three wildlife teams are continuing to search for oiled wildlife at the southern end of Motiti Island.
MAKO SHARKS
* Fastest of all shark species in the world, can swim at speeds of 90 km/h when hunting.
* Can sometimes be seen leaping out of the water.
* Feed primarily on tuna and swordfish, but will eat nearly everything.
* Aggressive by nature, they have been known to attack humans although they don't eat people.