NIA sources confirmed the searches, but did not divulge any details.
The agency had on April 27 filed a charge sheet in the Ernakulam NIA Special Court against two college students Allan Shuaib (20) and Thwaha Fasal (24), who were arrested and another absconding accused C P Usman, 40 in the maoist case.
It had said "the investigation had revealed that all the three are members of the proscribed terrorist organisation CPI(Maoist) and had conducted secret meetings and unlawful activities for furthering the cause of the outfit.
Thwaha and Allan, who were arrested by state police last year under the Unlawful Activities Prevenention Act (UAPA), were students of journalism and law respectively and the CPI (M)'s branch committee members in Kozhikode district.
Subsequently, the case was taken over by the NIA.
Meanwhile,the police conducted a search on Friday at the house of C P Jaleel, a Maoist, who was killed in an encounter in Wayanad in March last year.
The CPI(M) had in February expelled Allan and Thwaha from the party for their alleged Maoist links.
According to Malappuram Superintendent of Police, U Abdul Kareem, the search was conducted on a tip off that few affiliates of Jaleel and his brother were staying in the house at nearby Pandikkad.
"Other than the family of Jaleel, three men and three women were found in the house. Three of them were relatives of the family and three are outsiders," the SP told PTI.
Some documents and electronic gadgets have been recovered from Jaleel's house, the officer said.
"No one has been arrested. The police team has recovered few pamphlets, phone memory cards and few sim cards from the house. We are keeping a vigil on them," he said.
Jaleel along with three other members of his armed gang had arrived at a resort in Lakkidi demanding food and money.
He had been shot dead in a police encounter in March last year.
Maoists living inside the forest bordering Karnataka and Tamil Nadu often make flash visits to nearby markets in Wayanad and Malappuram districts to mobilise food materials from residents and shops in the vicinity.