English daily Bali Times said the suspension is now in effect following a Ministry of Law and Human Rights decree issued on June 7.
Authorities recently launched a crackdown on visitors found posing naked for photos at sacred sites, driving motorbikes without helmets and committing crimes.
There is also a threat of diseases carried by people coming from countries not certified as disease-free by the World Health Organization, the ministry said in a statement.
All tourists must obtain a visa from Indonesian missions abroad or electronically.
"By temporarily halting visa-free visits, the government aims to mitigate the potential risks associated with individuals entering the country without proper scrutiny and documentation," the ministry added.
Since 2016 Indonesia has waived visa requirements for travelers from 169 countries, including 10 ASEAN countries.
Only nationals of ASEAN countries Brunei, the Philippines, Cambodia, Laos, Malaysia, Myanmar, Singapore, Thailand, Timor-Leste, and Vietnam now remain exempt from the visa requirement.
Intra-ASEAN travel is visa-free and visitors can stay in Indonesia for up to 30 days with a confirmed return ticket.