AFPTV footage from Friday showed Palestinians inspecting the blackened and partially charred interior of the al-Nasr mosque -- a landmark in Nablus' Old City.
Witnesses interviewed by AFP said the military operation took place between 2:00 am and 6:30 am.
When contacted by AFP, the Israeli army did not immediately provide official comment on its operations in the northern West Bank city.
Local religious authorities said a total of six mosques had been targeted.
The destruction came as Muslims marked the first Friday of the holy month of Ramadan.
In a statement, the Palestinian Ministry of Endowments and Religious Affairs called the damage to the Nablus mosques "a serious attack in its size and timing", and condemned "a systematic plan... in the desecration of our holy sites, mosques and places of worship".
Nablus endowments director Sheikh Nasser Al-Salman denounced "the Israeli occupation's barbaric invasion of Nablus mosques".
In a statement, he accused Israel of "working hard to violate Islamic holy sites and mosques at an accelerated pace".
Israel has been waging a weeks-long offensive in the northern West Bank that began around refugee camps regarded as bastions of Palestinian militancy.
It has since expanded to more areas, displaced tens of thousands of people and saw the first deployment of Israeli tanks in the territory in 20 years.
In a statement, the Nablus municipality condemned Israeli forces' "burning of the al-Nasr mosque, which is considered a historical mosque and an important heritage landmark inside the Old City".
Nablus municipality mayor Husam Shakhshir said Israeli forces had obstructed firefighting crews and prevented them from reaching the scene of the fire.
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