Yaalon on Sunday delivered a speech to senior officers in which he implored them to "continue speaking your minds".
"Do so even if your remarks aren't part of the mainstream, and even if they are at odds with ideas and stances held by the senior command or political echelon," Yaalon said.
His remarks were perceived as a public show of support for Major General Yair Golan, deputy head of the armed forces, who on the eve of Holocaust Remembrance Day this month made remarks comparing contemporary Israeli society to Nazi Germany.
Netanyahu had criticised the deputy chief of staff's "outrageous" remarks as "utterly mistaken and unacceptable", adding however a few days later that "the affair is behind us".
Sources described by Israeli media as "close to Netanyahu" said following Yaalon's speech the premier was surprised his defence minister was raising the issue of Golan's speech again, and Netanyahu summoned Yaalon to a meeting today.
A statement released by Netanyahu's office late Sunday reiterated that Golan's comparison was an "inappropriate remark" that harmed Israel internationally.
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