Parrikar was responding to a question related to recent revelation that Indian Mujahideen co-founder Yasin Bhatkal had lived in Goa during 2011-12, which went unnoticed by state police.
"I agree that Goa is being used by unwanted elements as a resting place," Parrikar, who also holds Home Portfolio, told the Legislative Assembly.
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The Chief Minister said from December onwards the state government will ensure that all hotels maintain updated record of guests, and those who fail to comply will face appropriate action.
During the Question Hour, Parrikar told the House that the National Investigation Agency (NIA) did not share any information with state police about the stay of Yasin in Goa.
"What we have come to know about NIA's investigation and about Yasin Bhatkal was through people," the Chief Minister said.
He claimed that Yasin did not visit Goa after 2011-12.
Yasin was arrested from the Indo-Nepal border in north Bihar after being on run for five years in August this year.
"Yasin had stayed in Goa before this government took over. After 2011-12, he never came to Goa," the Chief Minister said responding to a query by Congress legislator Jeniffer Monserratte.