The arrested person was identified as Mohammad Salim, who had been absconding since 2002. He was accused of waging war against the country.
"Mohammad Salim was arrested from Rajasthan's Tonk town by our team in the 2002 case of waging war against the country," an ATS statement said.
Salim had given shelter to one Samirkhan Pathan in Rajasthan, after the latter murdered a police constable in Gujarat to avenge the 2002 riots, the statement added.
It said that police had earlier arrested 13 people in the case and Salim was arrested from Tonk on the basis of information.
Salim will be handed over to Ahmedabad city crime branch, which is investigating the case.
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