In a state of the nation address he also said Indonesia was "actively involved" in seeking a peaceful solution to the broader regional dispute about ownership of islands in the Sea.
Widodo's underscoring of Indonesia's sovereignty over the Natunas islands - and the resource-rich waters surrounding them - comes at a time of high maritime tensions between Beijing and Jakarta after repeated clashes there.
"We are developing regions like Entikong, Natuna, and Atambua so the world can see that Indonesia is a big country, and every inch of its land and water is truly taken care of," he said in a televised address which did not refer directly to China.
His comments come as Jakarta prepares to mark independence day celebrations tomorrow by scuttling dozens of foreign boats seized for illegally fishing in Indonesian waters.
The government has previously said that Chinese ships would be among those scuttled. The sinking in May of a large Chinese vessel ship caught fishing illegally around the Natunas drew a sharp rebuke from Beijing.
Unlike several of its Southeast Asian neighbours, Indonesia has long maintained it has no maritime disputes with China in the South China Sea and does not contest ownership of any territory there.
After one such encounter in June, Widodo visited the Natunas on a warship. His defence minister has since outlined plans to improve an airstrip and deploy surface-to-air missiles, drones and other military hardware to the remote islands.
In his wide-ranging address Widodo also warned that Indonesia must respect human rights or risk failing to become a "productive, developed, or winning" country.
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