It was the first crash of an Algerian military plane since February 2014, when a US -built C-130 Hercules turboprop slammed into a mountain, killing at least 76 people and leaving just one survivor.
The news outlet added the crash is the biggest disaster in the history of the Algerian Air Force.
The group is fighting for the independence of neighbouring Western Sahara, a territory also claimed by Morocco in a long-running dispute. The plane came down in an open farm field near the base, the ministry says.
"There are more than 100 deaths".
Many people are feared dead as a military plane crashed in Algeria, local media reports.
The crash site of Air Algerie flight AH5017 is seen near the northern Mali town of Gossi, July 24, 2014. The crash killed 77 people.
FLN Secretary General Djamel made the comment to private broadcaster Ennahar TV but gave no total death toll in the crash, which happened outside Algiers.
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Footage from the scene showed thick smoke being emitted from the wreckage.
He said the Russian-designed Il-76 military transport plane was carrying soldiers. The plane reportedly crashed into a field in an agricultural area.
The cause was unclear and an investigation has been launched, the country's defense ministry said in a statement.
Since the crash was first reported, the death toll climbed sharply Wednesday, as emergency and military crews worked at the scene. It is widely used for both commercial freight and military transport.
Around 100 Algerian military personnel were on board an army plane that crashed on Wednesday near an airbase outside the capital, a military source told AFP.
The C-130 Hercules transport aircraft came down in the mountainous Oum El Bouaghi region.