A report Tuesday in the newspaper O Globo comes just three days after top International Olympic Committee officials ended week-long meetings in Rio, saying they had been "reassured" that severely polluted Guanabara Bay would be suitable for Olympic sailing when the games open.
O Globo said 10 rubbish collection boats were out of service because of a lack of funding from Rio's state government. It said that some barricades to keep household waste from reaching the bay also lacked funding.
The paper quoted Carlos Minc, the former secretary for the environment for the state of Rio de Janeiro.
Water quality has become a hot-button issue for Rio. Several Olympic-medal winning sailors have said it's the dirtiest place they have ever competed, citing incidents of dodging floating sofas, dead animals and plastic bags.
Rio Governor Luiz Fernando Pezao said recently that 49 per cent of the area's sewage is being treated, a number repeated last week by IOC officials.
A year ago the figure was reported to be about 30 per cent. Olympics officials say they believe a goal of treating 80 per cent can be reached in 17 months when the games open.
In December a drug-resistant "super bacteria" normally found in hospitals was also discovered in the water around the bay.
Fish die-offs are also common in Rio's Rodrigo de Freitas Lake, where the Olympic rowing competitions will be held.
Severe water pollution also plagues the lagoon that touches the Olympic Park — the heart of Rio's games — and the new Olympic golf course.
Aerial photos taken last week by the environmental group Olho Verde showed a massive bacterial bloom inside the lagoon that has spilled into the Atlantic and a popular nearby beach.
Nawal El Moutawakel, head of the IOC inspection team, said last week she was assured by government officials that the problem was being tackled.
"We want every single venue to be ready for the athletes to compete in a secure and safe manner," she said. "We have been given reassurances that all the venues will meet the level ... so athletes can compete."