An FIR under various sections of Official Secrets Act and Indian Penal Code was registered against the accused today.
The ATS had been keeping a close watch on the duo after learning about their suspected role as spies for the Pakistan's intelligence agency ISI, officials said.
They have been identified as - Alana Hamir Sama (40), a resident of Kukma village of Bhuj taluka, and his associate Shakoor Sumra (38), resident of Sumrapor in Bhuj taluka of the district.
"We nabbed the duo last night when they came to Bhuj bus station to discuss about sharing of more information with ISI," he said.
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According to an official release by the ATS, a mobile phone made by a Pakistani company was recovered from Alana, who was in touch with ISI since last two years.
Both of them are now being questioned in Bhuj by various state and Central agencies to dig out more information from them, it said.
The action comes amid tension between India and Pakistan after the recent surgical strikes by the Indian Army on terror launch pads across the LoC. A high alert has been sounded in Gujarat, specially in border areas due to the threat of terror attack.