Authorities have sealed several properties belonging JeI, including residences of some of its activists, police said on Saturday.
The massive raid comes days after the government of India banned the outfit on grounds that it was "in close touch" with militant groups and was likely to "escalate secessionist movement".
Several properties, including residential houses, belonging to various JeI leaders and activists were sealed in many areas of the city and elsewhere in the Valley Friday night, a police official said.
Bank accounts of JeI leaders have also been freezed.
Various district magistrates have also sought list of moveable and immovable properties of the Jamaat leaders, he said.
However, it was not clear if the move was linked to the ban on JeI or was done by NIA in connection with its probe into money-laundering cases.
The separatist group was banned by government under anti-terror law on Thursday.
This came days after the security forces launched a crackdown on separatist groups in the state and arrested several leaders of Jammer-e-Islami, in the wake of the February 14 Pulwama terror attack in which 40 CRPF personnel were killed.
The group was banned Thursday as an unlawful association under the Unlawful Activities (Prevention) Act for alleged anti-national and subversive activities, officials said.
A notification on the ban was issued by the Ministry of Home Affairs (MHA) after a high-level meeting on security, chaired by Prime Minister Narendra Modi.
In the notification the Centre stated it is of opinion that Jamaat-e-Islami is in close touch with militant outfits and is supporting extremism and militancy in Jammu and Kashmir and elsewhere.
The separatist group is alleged to be involved in anti-national and subversive activities in the country.
The Central government is of further opinion that if unlawful activities of JeI are not curbed immediately, it is likely to escalate its subversive activities.