The court annulled the defence minister's decision of Nov. 22, 2016 on the colonel's suspension from his duties as Air Force commander.
"There were no legal and factual grounds for the appellant's suspension," Judge Marius Bajoras told BNS.
"The court made this conclusion because at the time the contested order was issued the applicant was neither suspected of committing a disciplinary offense nor named a suspect or an accused in a criminal case," he said.
The same court on Jun. 12 closed the colonel's case as he had already been reinstated in his post. It also stated that the case did not fall within the competence of an administrative court. A higher court, however, overturned this ruling.
The Defence Ministry has said that Navickas failed to enforce the Defence Resource Council's decision, made in February 2016, not to repair military helicopters in Russia.
Navickas earlier this year was reinstated in his post only to be dismissed shortly afterwards. Lithuanian Defence Minister Raimundas Karoblis has dismissed him from professional military service
The Defence Ministry said that the decision to discuss the Air Force commander was based on military intelligence information that he had "belittled" the defence minister and the chief of defence and sought to discredit the national defence system.
The process of sending Mi-8 helicopters to Russia for an overhaul was cleared by several high-ranking defence officials before it was stopped at the last stage in 2016.
The Foreign Ministry says that helicopter repairs in Russia would have run counter to the European Union's decisions on sanctions against Moscow and to Lithuania's foreign policy.
Dainius Guzas has replaced Navickas as the Lithuanian Air Force commander.