Rahman was running the madrasa at Tangi, 25 km from here, for the past two years and had appointed five teachers.
"While 56 students left for their homes today, three and 12 students had vacated the madrasa on Thursday and Friday respectively," District Child Protection Officer Pragati Mohanty said.
Most of them were from Jharkhand and the authorities ensured that all of the students were handed over to their guardians after verifying their identities, Mohanty added.
Rahman was very close to these teachers and spent a lot of time with them, sources said.
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It was found that the al-Qaeda facilitator had taken the piece of land for the madrasa at a deserted place in Tangi on lease from one Shiraj-ud-din, a businessman of Cuttack city, the sources added.
Meanwhile, the city police after booking Rahman under Unlawful Activities (Prevention) Act on Friday are now planning to send a team to Jharkhand to investigate his alleged involvement in motivating youths to join the terrorist organisation.
The police also continued to verify the banking transactions of Rahman for the third day today.
He reportedly operated three bank accounts in two local branches of two nationalised banks which have overseas branches in London.
A bank officer on condition of anonymity said that huge amounts were credited to one of his accounts twice recently through National Electronic Fund Transfer (NEFT) and Rahman withdrew the amount in phased manner.