Pandji Pragiwaksono came out of Jakarta's police headquarters on Friday evening about seven hours after going in.
Police said he had been summoned but did not name him as a suspect in any offence or mention any formal charges.
"I tried to answer the police's questions as best as I could and I don't think I had committed religious blasphemy," he told reporters.
"I will just follow the legal process," he added.
Pragiwaksono's show appeared on Netflix on December 27 and included satirical comments on Indonesian politics, including the 2024 election.
That vote was won by former military general Prabowo Subianto, who has now become president of the world's most populous Muslim-majority country.
Pragiwaksono also criticised Indonesia's two largest Muslim organisations, Nahdlatul Ulama and Muhammadiyah, for receiving a mining concession from the government when Joko Widodo, known as Jokowi, was still president.
Both denied any wrongdoing at the time and said the concessions would improve the welfare of their members.
The nearly two-and-a-half-hour Netflix show has divided opinion in Indonesia.
Some have accused the comedian of insulting religious entities and state institutions while democracy activists have defended him.
"Yes, today we are clarifying several things based on five police reports," Jakarta police spokesman Andaru Rahutomo said.
Two of the five police reports were filed by people who said they were members of the youth wings of Nahdlatul Ulama and Muhammadiyah, and said that the comedian had committed blasphemy and defamed their organisations, police said.
Both organisations said they had no links to the individuals listed on the police complaint.
