Army sources said that Major Sharyf Bhonsle had gone to Spain allegedly without informing the authorities concerned about his it.
He had taken leave in June and was supposed to report back on duty in August but he did not, they said.
Initial inputs suggested that he was taking part in adventure games and had injured himself, but there was no information after that, the sources said.
The sources said his family as well as his unit did not have any information about him.
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Following this, an Army Court of Inquiry was set up at the Para Regimental Centre, Bangalore, which declared him an absconder, the sources said.
The case will now be handed over to the police in Arunachal, where he was posted, or in Pune, where he hailed from, the sources said.
They said that the officer had not sought clearances from the Military Intelligence (MI) as is the rule for all serving officers to travel abroad.
The Special Force Units of the Army are mandated with special operating missions such as hostage rescue, counter-terrorism, unconventional warfare and special reconnaissance.