Local fisherman Sandy Stoddard said the dive crew searched the hull, but came up empty handed.
He said the vessel is badly damaged.
Police were sending HMCS Glace Bay with the Fleet Diving Unit and a remotely operated vehicle (ROV) to help search the site.
HMCS Glace Bay left Halifax for the overturned boat. Police are expected to carry out a ROV underwater assessment on Sunday.
The Mounties in Woods Harbour said aircraft observed the hull of Miss Ally around 10 a.m. on Saturday. Crews reached the site after 12 p.m. local time.
The boat was 129 nautical miles southeast of Halifax.
"The water depth is 900 metres and combined with sea and weather conditions the location of the hull further complicates efforts to investigate the submerged portion of the hull," said Cpl. Scott MacRae.
George Hopkins, whose son Joel Hopkins is one of the missing fishermen, said the boat is overturned and intact.
Formal search ended Tuesday
The formal search for crew members Billy Jack Hatfield, Joel Hopkins, Katlin Nickerson, Steven Cole Nickerson and Tyson Townsend was called off Tuesday night after officials concluded there was little hope any of the men would have survived the rough seas and cold water.
A private fishing boat continued the search.
A joint operation involving Department of National Defence and Canadian Coast Guard crews had launched an extensive search for the vessel on Thursday morning after families and friends pleaded with authorities to keep looking.
On shore the family and friends of the lost fishermen waited anxiously at a community centre all day, reported the CBC's Michael Dick.
Hopkins said finding bodies would give him closure.
The 13.5-metre vessel, which was on an extended halibut fishing trip, was last spotted by the coast guard on Tuesday, floating upside down more than 100 kilometres offshore.Suggest a correction