The Greenpeace protest at the Albian Sands oilsands site north of Fort McMurray, Alta., ended peacefully Wednesday afternoon after the company and RCMP agreed to let the protesters leave without facing any charges.
The deal was revealed after protesters met with Shell officials and the RCMP.
"As long as we removed ourselves, (they) agreed to release us without any charges, either criminal or civil," said Mike Hudema of Greenpeace.
On Tuesday, activists from Canada, France and the United States chained themselves to a three-storey truck after sneaking onto the Muskeg River mine site around 8 a.m. local time.
A second group of protesters unfurled a banner on the ground that said, "Tar Sands: Climate Crime." By the end of the day, the group occupied a second giant truck.
The protesters left around 4 p.m. Wednesday.
The protest was timed to coincide with a meeting between Prime Minister Stephen Harper and U.S. President Barack Obama on Wednesday in Washington.
In a news release, Shell explained the reasons for the agreement with the protesters.
"Shell has agreed not to pursue criminal charges against the protesters because it does nothing to further the climate change conversation," said John Abbott, Shell's executive vice-president of heavy oil. "We rely on democratic processes to determine Canadian CO2 policy and other important matters.
"We invited Greenpeace to discuss their climate and energy views with us directly but they chose not to do so, which is disappointing."
It is not clear how the activists entered the site undetected. Shell said it is doing a full audit of security and has "significantly" increased it.
Shell temporarily suspended operations at part of the Muskeg River mine site on Tuesday because of concerns for the protesters' safety. The company ramped up production later in the afternoon.