At least 16 people were killed and 18 others injured in the accident near El-Tor in southern Sinai, some 300 kilometres southeast of the capital Cairo.
The Sinai Peninsula has been a hotbed of militancy for years but security forces also face accusations of human rights abuses.
"Amid ongoing efforts in pursuing and defeating terrorist elements ... during the previous period, the armed forces ... carried out operations that killed 89 dangerous takfiris (militants) ... in northern Sinai," the army spokesperson says.
At least eight members of the international group Multinational Force and Observers, including six Americans, have died in the crash.
The Egyptian army is short on military successes, and that history may give some military officials pause for thought.
Egypt is sounding the drums of war in Libya, but any military incursion faces daunting military and political obstacles.
Palestinians are vocal in their opposition to US President Donald Trump's Middle East plan, which gives Israel the green light to annex Jewish settlements and other strategic territory in the West Bank.
Egypt has been fighting the Sinai affiliate of the Daesh extremist movement for years and struggling to re-establish control over the restive border region.
The ‘Deal of the Century’ has gone back on years of promises and negotiations that Palestinians have already endured, and rejected.
Egypt's interior ministry said they killed at least 17 militants in raids in Cairo and in Fayoum, four days after a car filled with explosives wrecked outside the county's main cancer hospital, killing at least 20 people.
Militants attacked forces stationed south-west of the city of Arish, the Egyptian interior ministry said in a statement.
At least eight Egyptian security personnel were killed on Wednesday in the Sinai Peninsula, the centre of a long-running militant insurgency, the interior ministry confirmed. Other sources place the death toll at 10 officials.
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