Defence Minister Peter MacKay said starting Thursday, military officials will actively check in with provincial authorities to see if help is still needed in an ongoing case.
The onus has previously been on provincial authorities to ask for extra assistance.
"I believe the adoption of this new protocol improves communication and enhances situational awareness among all ... search and rescue agencies," MacKay said during a conference call from Ottawa.
"Working together we will continue to ensure one of the best search and rescue systems in the world."
He said the change is already in effect in Newfoundland and Labrador and will eventually be expanded across Canada.
Ottawa launched a protocol review after questions were raised about why it took two days for military aircraft to join the search for Burton Winters of Makkovik.
Winters's body was discovered on Feb. 1 on the frozen Labrador Sea, a few days after the 14-year-old boy was reported missing.
The military has said there was no chopper available to search for the boy when the first request for help came in on Jan. 30. It also said the cloud ceiling was too low for military flight in the region.
Two military aircraft arrived the following day after local searchers made a second request for help.
MacKay said he realizes the change in protocol won't bring closure to Winters's family and friends.
"It's obvious this has been a very difficult time for the family and friends of Burton Winters and the entire community of Makkovik," he said.
"But I do hope that it reassures the community that professionals are always evaluating and working together, and that our search and rescue capabilities are always looking for ways to improve."
MacKay stressed that in the case of ground search and rescue efforts, military aircraft should only be used when no other option is available or when the requirements of the search can't be met by provincial authorities.