Anu Rannaveski has been appointed to lead the Defense Resources Agency (KRA) by Minister of Defense Hanno Pevkur (Reform).
Rannaveski, who has worked at the Ministry of Defense since 2011, took over the role on Monday.
She replaces Marlen Piskunov who resigned in March and whose duties she has been covering since then.
Pevkur said Rannaveski is an experienced expert in the field.
The job application process was criticized because it required candidates to have a master's degree, a qualification Rannaveski has. Only one application was submitted by the deadline.
State Secretary Taimar Peterkop said in September this requirement made the process look as though the Ministry of Defense already had someone in mind for the position.
"But the Ministry of Defense remained adamant that this requirement is needed for this position. But I completely agree that such an impression remains," he told ETV's debate program "UV faktor".
The KRA calls up and prepares citizens for compulsory military service, recruits citizens for duty in the active service, ensures an overview of the state's available mobilization resources and supports the national defense course in schools.
Editor: Helen Wright