Indonesia has confirmed more than 1.6 million cases and 46,000 deaths from COVID-19, the largest totals in Southeast Asia.
Although 1st-time violators of Bali's mask-wearing rule face fines of 1 million rupiah for foreigners and deportation after a second offense, the police wanted them removed off the island immediately.
The wreckage is located 1,500 meters (yards) to the south of the site where the submarine last dove Wednesday, off Bali's northern coast.
The navy had previously said an electrical failure could have left the submarine unable to execute emergency procedures to resurface.
With the authentic evidence we found believed to be from the submarine, we have now moved from the sub miss phase to sub sunk, Indonesia's Navy Chief Yudo Margono said.
The vessel's collapse depth was estimated at 200 meters (655 feet) by a South Korean company that refitted the vessel in 2009-2012.
India is one of the few countries that have a naval force capable of complex missions in the deep waters.
Frank Owen, secretary of the Submarine Institute of Australia, also said the submarine could be at too great a depth for a rescue team to operate.
Military chief Hadi Tjahjanto says the KRI Nanggala 402 was participating in a training exercise on Wednesday when it missed a scheduled reporting call.
Rahmat Triyono, the head of Indonesia's earthquake and tsunami center, said in a statement the undersea earthquake did not have the potential to cause a tsunami.
Local authorities declared a state of emergency for East Nusa Tenggara -- among Indonesia's poorest provinces and the epicentre of the disaster -- until early May.
East Flores district on Adonara island suffered the highest losses with 67 bodies recovered so far and six missing.
Hundreds of police, soldiers and residents dug through the debris with their bare hands, shovels and hoes searching for those buried.
Search and rescue teams in Indonesia were racing to find more than 70 people still missing and using diggers to clear mountains of debris.
Indonesia's disaster agency said that downpours are expected over the next day as the storm triggers offshore waves as high as six metres.