The three accused - Khalid Mahmood, Irshadul Haque and Muhammad Shoaib - were yesterday presented before ATC-2 judge Bushra Zaman in Gujranwala, some 70 kms from here, in the Punjab province.
The judge granted six-day 'physical remand' of the suspects and handed them over to the Counter-Terrorism Department (CTD) police, the Dawn reported.
They are said to be involved in the January 2 attack on the key Indian Air Force base in Pathankot.
The three suspects denied the charges and were shifted to an undisclosed location for investigation.
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The CTD earlier this month registered an FIR against the unknown attackers in Gujranwala.
The FIR number 06/2016 was lodged under sections 302, 324 and 109 of the Pakistan Penal Code, and sections 7 and 21-I of the Anti-Terrorism Act.
It is not known when the three were arrested but it is believed that that might have been arrested well before the registration of the FIR and probed which provided enough evidence to proceed against them in the court of law, officials said.
Several alleged militants were arrested after the attack for which India blamed JeM.
India has also provided leads with phone numbers which have been included in the FIR.