Montreal police said the three, who climbed the giant globe-like structure to hang a banner, will be in court next February on mischief charges.
Police didn't have to scale the structure as the ecologists came down on their own and surrendered after several hours perched from the federally owned environmental museum.
The peaceful protest will not be the only one, a Greenpeace spokesman vowed from the foot of the structure.
"Greenpeace will not be silent," said Patrick Bonin. "Greenpeace will continue to take part in actions of peaceful civil disobedience as it has done for the past 42 years."
The three Montreal protesters were released on a promise to appear on either Feb. 20 or 21.
The action was in support of a group arrested during a demonstration in mid-September.
Two Canadians were among 28 Greenpeace activists detained by Russian authorities at a Gazprom oil-drilling platform in the Arctic Circle more than two months ago.
A Russian photographer and a British videographer were also arrested.
Nearly half have been granted bail while awaiting trial, but it's unclear if the foreign activists will be allowed to leave the country because they don't have their passports, which were seized by authorities.
They were charged with piracy but authorities have since downgraded the charge to hooliganism, which carries a maximum seven-year prison sentence.
One of the two Canadians — Quebecer Alexandre Paul — remains behind bars while Ontarian Paul Ruzycki was granted bail earlier this week. Paul is expected before the court on Thursday in Russia for his own bail hearing.
Paul's parents were at the Biosphere on Wednesday and spoke in favour of his release.
Bonin said Greenpeace is surprised by the silence of the Harper government, which it says still has not publicly intervened to denounce the attitude of the Russian government in the arrests.
The organization said countries like Britain, Germany and France as well as a collective of Nobel Prize recipients have said they support the release of the detainees.
"Clearly, the federal government could take a public position, at the very least, establish a dialogue with Greenpeace on a political viewpoint," said Bonin.
Thus far, the government has said it is offering consular services to the two Canadians and keeping an eye on the legal proceedings.
- With files from Associated PressSuggest a correction