The ban was lifted for companies which had complied with export rules, Maritime and Investment Coordinating Minister Luhut Pandjaitan told reporters, without saying how many companies were allowed to resume exports.
Bambang Gatot Ariyono, director general of Minerals and Coal at the mining ministry said the government has been investigating more than 30 companies.
Indonesia, the world's largest nickel ore exporter, temporarily stopped ore shipments on Oct. 28 following reports that monthly exports had surged nearly three-fold after the government announced it was bringing forward an export ban by two years to January 2020.
The exports also reportedly included large amounts of high-grade ores, which are not allowed to be shipped under the rules.
Earlier on Thursday, investment board chief Bahlil Lahadalia said he would hold a meeting with nickel companies on Monday to discuss whether to resume wider shipments of nickel ore.
Pandjaitan added that Lahadalia would give more details about the recent review of violations at that time.
At least 20 nickel ore vessels were being held in ports due to the halt in exports, said Meidy Katrin Lengkey, secretary general of Indonesia's nickel miners association (APNI).
(Reporting by Bernadette Christina Munthe; Writing by Fransiska Nangoy; Editing by Emelia Sithole-Matarise and Kirsten Donovan)