According to arabi21.com website, the Abu Refaei Mosque in Sheikh Zuweid, a Bedouin town in the North Sinai Governorate, was attacked by the military on Thursday.
Copies of the Quran and Islamic books inside the mosque were also damaged as a result of the attack.
Photos of the damages were posted online on Saturday.
It is not clear why the military has attacked a place of worship.
Over the past several years, Egyptian troops have been engaged in efforts to quell rampant militancy across the Sinai Peninsula.
The battle has led to the deaths of hundreds of troops and militants, including those with Takfiri groups.
In October 2014, a state of emergency was declared across the whole peninsula following a deadly terrorist attack that claimed the lives of 33 soldiers.