Searches were also being carried out in Tral in Pulwama district at ancestral house of suspended Deputy SP Davinder Singh, sources said.
The J&K police has denied reports by sections of media that searches were carried out at an IPS officers residence in Shopian.
"News reports on NIA searches at IPS officer's residence in Shopian is fake," SSP Shopian Sandeep Chaudhary told .
On Sunday, the National Investigation Agency and the state police carried out fresh raids on locations of DSP Devinder Singh, Hizb terrorists Naveed Babu and Rafi Ahmad and a law school dropout Irfan Ahmad.
On Saturday a 20-member NIA team arrived in Kashmir to collect more facts about Davinder Singh who was arrested by J&K police while transporting three people including two Hibzul Mujahideen militants, Naveed Babu and Rafi Ahmed, and Irfan Amad to Jammu on January 11.
The team led by a DIG rank officer went to Anantnag and held a meeting with the police officials, sources said.
NIA officials are currently interrogating Singh in Jammu after the agency got his transit remand.
Last week the DG NIA, Y.C. Modi, reviewed investigations into the case that has shaken the security establishment.
After initial investigations by J&K police the case was handed to the NIA.
According to sources Babu, Ahmed and Mir had planned a travel to Pakistan after reaching Jammu.
After Singh's arrest, J&K police conducted multiple raids at his residences in Srinagar.
Singh was posted with the anti-hijacking wing of J&K police in Srinagar, and was part of the security staff that received a group of foreign ambassadors who visited Kashmir last month, including the US envoy.
( With inputs from IANS )