"It is no secret that we have not yet found the way to work together on missile defence," NATO head Anders Fogh Rasmussen said after a meeting of the NATO-Russia council.
"However, ministerial discussions are valuable in addressing existing concerns and we need to continue to engage frankly and directly to overcome our differences."
Moscow fears that US-led plans for a missile defence system against attacks from outside Europe -- taken to mean from Iran or terrorist groups -- compromise its security.
"We failed to work cooperatively on this issue and Russian concerns are not being (taken into account)," Shoigu told a news conference after the meeting.
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"Before studying missile defence projects, we want to have assurances that this US missile defence system is not against Russia," he added.
At the same time, Shoigu said Russia would continue efforts to resolve the issue, praising the work of the NATO-Russia Council in promoting cooperation on shared concerns such as counter-terrorism and transparency in military exercises.
Rasmussen also highlighted such areas of cooperation as he chaired a regular meeting of all 28 NATO member defence ministers.