In a news release issued late Thursday the Mounties said a Canadian Armed Forces Hercules was joined by aircraft from Transport Canada and Provincial Airlines in searching an area of more than 1,700 sq. km.
Officials said small items of debris were sighted in an area near the last known position of the 13-metre Miss Ally which overturned sometime Sunday.
An initial analysis of photos taken during the patrol suggested the items were from the vessel.
The Mounties said they had consulted with the families of the fishermen who were given the surveillance photos.
Police said two RCMP officers had boarded the Canadian Coast Guard Vessel Sir William Alexander and had left Halifax for the debris field where the vessel would provide security until further plans were developed.
Officials said an additional overflight would be conducted by the military on Friday.
"This is devastating to the families and to the entire community. These men were deeply loved and the loss of their young lives will impact the hearts and souls of the fishermen and their community for many years to come," RCMP Supt. Sylvie Bourassa Muise said in a statement.
Earlier Thursday Grieving families in Woods Harbour, N.S., had emerged from a meeting with the RCMP at a local community centre, relieved to hear that the Defence Department agreed to return to the area to search for the upturned boat, last spotted by the coast guard Wednesday afternoon.
"I'm feeling elated right now," said George Hopkins, whose son Joel was aboard the Miss Ally. "At least we're doing something."
Federal search and rescue officials said it was up to the RCMP to decide what to do because the case was handed to the Mounties when the search for the men was called off.
Marlene Nickerson, whose son Cole was on the boat, said she wanted to thank the community for applying pressure on the government to launch a recovery operation.
"Hopefully we can bring 'em home," she said through tears. "I won't be pleased until I see him again."
Local fishing boats headed out from Woods Harbour to look for the boat, which flipped over as it was battered by 10-metre waves and winds approaching hurricane force.
Friends of the five lost men stood on the dock and called out to the departing boats, "Bring our boys home!"
Some along the wharf said they were angry that the military had ended the search late Tuesday without saying what they would do about the upturned vessel.
Tim Nickerson headed out in his boat after lunch, saying before he left that fishermen would step in when the government wouldn't.
"Somebody's got to do something," he said on the dock. "These are local boys and the boat is there — do something."
The missing crew — all of them under the age of 35 — were on an extended halibut fishing trip when the military was alerted by a water-activated distress beacon just after 11 p.m. Sunday.
Pastor Phil Williams at the Calvary United Baptist church in Lower Woods Harbour said the community rallied behind the families' call for a salvage operation.
"I would venture to say that if you took a poll you would have 110 per cent," he said. "(We) want Miss Ally brought up at all costs, expense, whatever. It's essential for peace and closure."
Pierre Murray, regional manager of operations for the Transportation Safety Board of Canada, said a team of investigators arrived in Woods Harbour on Wednesday.
Murray said they plan to review communications between the crew and family members, friends and search and rescue officials.
He said the safety board's investigators will also look at the boat's stability assessments, construction and inspections as well as the crew's experience and training. The vessel was built in 2006 and had to be inspected every five years.
"We're going to try to find out what was going on, what type of weather they were experiencing, if the boat was damaged or if it was taking on water," he said from Halifax.
"The difficulty is that we don't have a boat and we don't have survivors, so what we can do is try to get as much as we can right now."
Murray said the independent agency once recovered a small fishing boat from the bottom of the Bay of Fundy to help with their investigation into a sinking that claimed four lives. But he stressed that conditions were more favourable then.
"It was a bit different from going out there in the open sea and trying to recover a boat," he said.
In January 2004, the 9.7-metre Lo-Da-Kash, based in Maces Bay, N.B., was heading back from Campobello Island when it sank with four people on board. The Transportation Safety Board conducted a dive on the vessel in May 2004 and it was raised to the surface four months later and towed to shore.
— With files from Michael MacDonald and Melanie Patten in Halifax