The ministry of defence gave details of the toll later Saturday on public television.
It added that a number of “terrorists” had been “neutralised”.
The army recovered rocket launchers, a mortar and a large amount of ammunition as well as mobile phones, drugs and syringes, according to an earlier statement.
A senior local official had told AFP on Friday that Boko Haram elements attacked Diffa.
He said the fighting had sparked “movements of panic” among the population of 200,000 but that calm had returned.
Diffa has been attacked several times since 2015. In May 2020 intense fighting broke out between the army and jihadists near the Doutchi bridge that links Niger with Nigeria, south of the city.
The region is also home to 300,000 refugees and displaced people who have fled jihadist fighters.
Fighting with Boko Haram and ISWAP jihadists has killed more than 36,000 people since 2009 and driven almost two million people from their homes in northeastern Nigeria.