Military sources said that armed men also attacked two public buses, injuring two passengers and robbing others, late on Thursday on the road between the main regional towns of Arlit and Agadez.
Around eight passengers were briefly kidnapped.
A senior military police officer said: "We have started search operations and everything is being done to find these attackers. It is the work of bandits who live off the backs of others."
The former French colony's desert north was the scene of a rebellion in the 1990s by light-skinned ethnic Tuareg, Arab and Toubou groups demanding more autonomy from a black African-dominated government.
Most groups accepted peace deals in 1995, but insecurity remains rife, with frequent acts of banditry, carjacking and kidnapping by former rebels who say they are still marginalised and accuse the government of failing to respect the accords.
On February 8, ex-rebel fighters attacked the town of Iferouane in the same northeast zone, killing three government soldiers.
The attack was claimed by a Tuareg group calling itself the Niger Movement for Justice (MNJ).
The group has demanded more Tuaregs be appointed to regional civilian and military posts and that income from Niger's natural resources be more fairly shared out.
Niger's government dismisses the fighters in the north as "highway bandits" and refuses to use the term "rebellion".
Despite being the world's third largest producer of uranium, Niger is one of the poorest nations on earth.