The armed assailants mingled with the convoy before opening fire on the military escorts on Sunday, the source said.
The soldiers chased the gunmen and "fell into an ambush which left five dead", the source said.
The convoy was heading for the town of Arlit from the gold rush site of Tchibarakaten 450 kilometres (280 miles) to the northeast where thousands of people have been drawn hoping to strike the precious metal.
A survivor of the attack told the Air Info online journal, based in the northern regional capital Agadez, that the assailants were "heavily armed" and laid an ambush.
The journal reported that five more soldiers were wounded.
An elected local official told AFP that "quantities of gold were probably carried off" by the attackers who "seem to have been well informed".
Attacks on gold miners have been frequent in the Agadez region where migrant, arms and drug trafficking is rife through Niger's vast swathes of desert bordering Libya and Algeria.
The impoverished Sahel country is grappling with a seven-year-old campaign by jihadists linked to Al-Qaeda and the Islamic State group.
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