Monte Alejandro Rubido Garcia, a high-ranking national public security official, was named by President Enrique Pena Nieto to succeed Manuel Mondragon y Kalb, a former Mexico City police chief who resigned on Sunday.
The Senate must vote to ratify the nomination of Rubido, a former senior official at the CISEN intelligence agency.
The National Security Commission was created by Pena Nieto in January 2013 to replace the public security ministry, which was in charged of the scandal-plagued federal police.
Under Mondragon's watch, Mexico was supposed to launch a gendarmerie force last year, but its debut was delayed until sometime this year.
Pena Nieto, who took office in December 2012, has maintained his predecessor's tactic of using marines and army soldiers to combat organized crime amid cartel wars that have left tens of thousands of people dead and missing since 2007.