Senior Sergeant Mike Cook, of Alexandra, said police were now looking for a body.
The victim's name has not been released by police.
Snr Sgt Cook said a police diver had flown in on Tuesday evening and spent yesterday assessing the situation.
Variables such as the river's depth, flow and water temperature had to be assessed.
Three more divers, from Wellington, will join the team today.
Search party members were called off the Clutha River at Roxburgh at 2pm yesterday because Contact Energy needed to release the large amount of water backed up behind the Roxburgh dam.
It was deemed too dangerous for the search to continue as the river levels rose.
Contact had dropped the river flow from 400 cubic metres a second (cumecs) to 260 cumecs, holding back the water so searchers could more easily see the bottom of the river.
The lower flow also exposed some of the area where the teenager was last seen.
Snr Sgt Cook said some of the rocks were as big as cars, and it was possible the body was caught among them. With the force of the water pushing against the body it would be unlikely to come to the surface, he said.
The visibility at midday had been "fantastic", with the sun directly overhead and no wind to ruffle the surface of the water.
Searchers on boats and jet-skis were able to see 2m into the water while the helicopter crew could see up to 6m below the surface of the river.
Since the body was not visible to searchers, it seemed likely it was caught under a rock, a log or a tree, he said.
Members of the teenager's family have arrived in Roxburgh.
They did not want to talk to the media.
The teenager was swimming with his friend, also from Dunedin, on Tuesday afternoon when he struck trouble.
When the victim disappeared under the water his friend had to climb a couple of steep banks and run across the road to find a house from which he could call for help.
He has now returned to Dunedin.
Snr Sgt Cook warned people not to swim in rivers they were not familiar with.
"If you are visiting a town find someone who knows the river, as although it may look picturesque it could spell danger."
Snr Sgt Cook told NZPA the missing youth was in the area for fruit-picking work and had family there.
