German Navy Chief Kay-Achim Schoenbach apologised for his "rash" comments, published on YouTube and widely circulated on German media, and called them a mistake.
In a Twitter post, Schoenbach said his remarks at a thinktank discussion in India expressed a personal opinion and not the official position of the defence ministry.
The remarks come at a sensitive time as Russia has amassed tens of thousands of troops on Ukraine's borders and diplomatic efforts are ongoing to prevent the situation from escalating into war. Russia denies it is planning to invade Ukraine.
A spokesperson for the Defence Ministry in Berlin said the remarks did not reflect Germany's position in either content or wording.
"Admiral Schoenbach will get the opportunity to express his views to the chief of defence," the spokesperson added.
In the video, Schoenbach, speaking in English, says Putin seeks to be treated at eye level by the West.
"What he (Putin) really wants is respect," Schoenbach says.
"And my God, giving someone respect is low cost, even no cost... It is easy to give him the respect he really demands - and probably also deserves," Schoenbach said, calling Russia an old and important country.
Schoenbach concedes Russia's actions in Ukraine needed to be addressed, but adds that "the Crimea peninsula is gone, it will never come back, this is a fact", thereby contradicting the joint Western position that Moscow's annexation of the peninsula from Ukraine in 2014 cannot be accepted and must be reversed.
The Ukrainian Foreign Ministry called on Germany to publicly reject the navy chief's comments.
Schoenbach's comments that Crimea would never return to Ukraine and that Russia's president deserved respect could impair Western efforts to de-escalate the situation, it said in a statement.
"Ukraine is grateful to Germany for the support it has already provided since 2014, as well as for the diplomatic efforts to resolve the Russian-Ukrainian armed conflict. But Germany's current statements are disappointing and run counter to that support and effort," Ukraine's Foreign Minister Dmytro Kuleba said separately in tweet.