The group was banned for five years under anti-terror law on grounds that it was "in close touch" with militant outfits and is expected to "escalate secessionist movement" in the state.
Shah said stringent actions would be taken against any individual who jeopardises the nation's security.
While Jamaat cannot take part in the elections due to the ban imposed on it by the Union home ministry, it had shown interest in participating in the polls during the Lok Sabha elections if the ban were removed.
The raids in the twin capitals of Srinagar and Jammu along with Budgam in central and Kulgam and Anantnag in south Kashmir led to the seizure of incriminating documents and digital devices connected with the activities of JeI and its related Trusts and more than Rs 20 lakh, a spokesperson of the federal agency said.
The Union home ministry said the Muslim Conference Jammu and Kashmir - Sumji faction, chaired by Ghulam Nabi Sumji, is known for its anti-India and pro-Pakistan propaganda and its members have been involved in supporting terrorist activities and providing logistical support to terrorists in Jammu and Kashmir.
Jamaat-e-Islami Jammu and Kashmir, a religiopolitical organisation on Wednesday asked tourists to follow a proper dress code or stop visiting the Himalayan Valley.
At least six bank accounts linked to the group have been identified and the banks concerned directed to immediately freeze them.
The detentions come ahead of a crucial hearing on Article 35-A in Supreme Court which is likely to take place on Monday. The article, incorporated into the Indian Constitution in 1954, grants special rights and privileges to the citizens of Jammu and Kashmir.
Gauba said the JKLF spearheaded the separatist ideology in Kashmir Valley and the action was taken following the 'zero tolerance' policy of the central government against terrorism.
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