Interior Minister Bernard Cazeneuve ordered the investigation as the government faced fierce criticism from the opposition over security for the July 14 event.
The head of the national police internal affairs division, Marie-France Moneger-Guyomarc'h, described the squabble as "the result of poor understanding and interpretation of information."
She said that 64 national police and 42 municipal police were deployed to secure a fireworks display on the Nice seafront for the July 14 national holiday.
Opposition politicians had contested the figures for police deployment, with regional president Christian Estrosi slamming "state lies".
President Francois Hollande is facing mounting demands to improve security after a string of terror attacks, dating back to January 2015, left at least 230 people dead and hundreds injured.
Pressure on Cazeneuve intensified when a local police officer, Sandra Bertin, accused his ministry of trying to bully her into altering a report on police deployment on the night of the attack.
Bertin is a strong supporter of Estrosi and has fiercely criticised the Socialist government through social media networks, Le Parisien newspaper reported Monday.
Cazeneuve filed a lawsuit for libel against Bertin, saying her accusations were "likely to give birth in the public mind to the idea that the ministry and the minister have communicated false information" regarding the Nice massacre.
