The National Investigation Agency (NIA) said it carried out searches at the three houses in the southern state of Kerala, located near the tip of the Indian peninsula.
The coordinated suicide bombings by Islamist militants at hotels and churches in Sri Lanka on Easter Sunday sent shockwaves through the Indian Ocean island state that had enjoyed relative peace since a civil war ended a decade ago.
"These persons are suspected to have links with some of the accused persons in the said case who had exited India to join the proscribed terrorist organisation ISIS/Daish," the NIA said in a statement, using other names by which Islamic State is known.
The investigators recovered mobile phones, SIM cards, digital storage devices including CDs and DVDs of radical Islamist preacher Zakir Naik and diaries with notes handwritten in Malayalam and Arabic, the NIA said.
Current and former state police officials told Reuters Islamist extremism hardly posed a threat in the state, which they said had a history of peaceful co-existence between the majority Hindu community and religious minorities."Compared to the large Islamic population, the percentage of people is a very small number, not at all a significant number," a senior state police official told Reuters.