"The majority of the footboards were already unstable, lifted or detached from the structure," West Manggarai district police chief Christian Kadang was quoted as saying by news site Kompas.com after investigators inspected the bridge at the Cunca Wulang Waterfall tourist site.
He said safety nets along both sides of the bridge were up to 90 per cent damaged or missing.
The two Austrian tourists, aged 55 and 57, died on Sunday after falling about 10 metres into a river gorge when part of the bridge gave way, according to rescue authorities.
Rescue teams later evacuated the bodies to a regional hospital in Labuan Bajo.
Authorities have seized visitor registration documents and management records as part of an investigation into the operation of the tourist site.
Christian said investigators were examining possible discrepancies between tourism fees collected from visitors and spending on maintenance and safety infrastructure.
Police also found that visitors were not accompanied by certified guides during trekking activities and that local staff had not received adequate tourism safety training, he said.
The accident has renewed scrutiny over tourism safety in Labuan Bajo, a fast-growing destination that Indonesia has promoted as one of its "super priority" tourism hubs outside Bali.Â
Located on the western tip of Flores island, Labuan Bajo serves as the main gateway to Komodo National Park, home to the endangered Komodo dragon and a major destination for diving and nature tourism.