Harper was met later in the day in Mill Bay, B.C., by about 100 chanting, placard-carrying protesters who stood across the road leading to Brentwood College School, where the prime minister was set to speak to Conservative Party supporters.
Several protesters jawed about public and private property rights with RCMP officers who formed a line nearby.
Others carried homemade placards displaying their opposition to the federal government's position on climate change or the proposed Northern Gateway pipeline, which would bring Alberta oil products to British Columbia's North Coast for export to Asia by tanker.
Many chanted, "Hey-ho, Harper's got to go."
Some of the placards stated, "B.C.'s Not a Carbon Producer," "Stop Harper," "Hands Off Our Wilderness, Oceans, Rivers and Scientists."
It's the second time protesters have disrupted Harper's plans on his swing through the province.
Two climate-change activists made it to the same stage as Harper during a question-and-answer event for a business crowd at a Vancouver hotel on Monday.
Vancouver police have announced the pair won't face charges, though questions are being asked about how the protesters could have come within an arm's reach of the prime minister during the Vancouver Board of Trade event.
Sgt. Randy Fincham said Vancouver police have consulted with the RCMP and determined criminal charges would not be appropriate.
The Prime Minister's Office and the RCMP have declined to discuss the specifics of what happened, though the Mounties are reviewing the incident
Protester David Trudel of Victoria said he came out to Mill Bay Tuesday to deliver a message to Harper that the government can't run roughshod over the rights of Canadians.
"I think yesterday's event in Vancouver made it clear that Stephen Harper is dismissive of this whole movement of people who are concerned, really concerned about the land, the water, environmental protections that have been stripped away by the Harper government," he said.
Harper did not mention the protesters or Monday's security incident during his speech to party faithful Tuesday.
More than 400 people crowded into the school auditorium to hear Harper say he will defend his majority government's record of economic, social and international achievements during the 2015 federal election campaign.
Harper took shots at the Opposition New Democrats and the federal Liberals led by Justin Trudeau.
"This country, Canada, is in a stronger position in the world economy today than it has ever been in its history," he said. "With the NDP and the Liberals, what you see is what you get: dangerous ideas on the one hand, vacuous ideas on the other."
Harper said his walk along the Trans-Canada Trail with his wife, Laureen, and the Scouts was designed to send a message that Canadians need to complete the cross-country trail in time for the nation's 150-year birthday in 2017.
Harper walked about a kilometre along the former rail-bed and crossed the Kinsol Trestle bridge, a former railway crossing high above the Koksilah River near Shawnigan Lake, B.C.
He said the wooden crossing is part of the 24,000-kilometre Trans-Canada Trail that winds through every province and territory.
Harper said the federal government will contribute one dollar to complete the cross-country recreational route for every two dollars raised by the Trans-Canada Trail Foundation.
The Kinsol Trestle is known as one of the world's largest and most spectacular wooden-railway trestles.
The curving 188-metre-long, 38-metre-high trestle once allowed steam trains to haul giant coastal cedars and firs out of the rainforest, but the last train crossed it in 1979.
Abandoned, left to rot for years, and destined to be torn down in 2006, the trestle was preserved by local residents who mounted campaigns to preserve its heritage value and as much of its original structure as possible.
Today, and more than $7 million later, the Kinsol Trestle is a link to hundreds of kilometres of idyllic walking, hiking, biking and horseback riding trails that form part of the nationwide Trans-Canada Trail.
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