The move came after a hacker was suspected of trading the data that contained foreign visas to enter Indonesia issued by the Directorate of General Immigration of Indonesia, Voice of Indonesia reported.
The director general of information and public communication at the Ministry of Communication and Information Usman Kansong said his agency was still checking information.
Last week, Indonesia also launched an investigation after a cybersecurity practitioner revealed the data of 34 million Indonesian passports had been allegedly leaked and traded.
The information in the leak contained data ranging from the passport registration number and valid date, to full name, date of birth and gender. The data was sold for US$10,000.
Since 2016 Indonesia has waived visa requirements for travelers from 169 countries, including 10 ASEAN countries.
The country has stopped the visa-free entry citizens of 159 countries and territories outside ASEAN amid concerns about "disruption of public order and potential transmission of diseases."