Greenpeace should not "raise a clamor but [work to] minimize ecological risks should they appear," Putin said in a statement published Thursday by state news agency RIA Novosti.
Thirty people were arrested in September after Greenpeace activists scaled a drilling platform in the Russian arctic. The group was using its Arctic Sunrise ship to campaign against Gazprom's operations in the northern Pechora Sea.
Gazprom's Prirazlomnaya rig was towed to the region last year as the first ice-resistant oil rig in the world. Greenpeace said it was concerned about the potential for an oil spill in the harsh arctic environment.
The detained Greenpeace activists are to be released as part of a general amnesty measure signed by Putin this week.
Putin said he encouraged dialogue with the environmental group, not high-profile demonstrations.
"We are open to joint efforts, including with Greenpeace," he said.