There have been no civilian casualties or collateral damage, the Army said.
12 security personnel, including three officers, were also injured in the operation at Reasi.
The 3 arrested were in continuous touch through WhatsApp with Maulana Mufti Ashghar, based in Muzaffarabad, whose nephew Waqas (JeM commander in South Kashmir) was killed in an encounter near Pulwama recently.