The Malaysian crashed out in the first round with food poisoning and voiced fears that players could stay away from the Hyderabad world championships in August if safe food and water could not be guaranteed.
"I was told to be careful of the food we take in India but I never thought it would happen to me. In fact, Wong Mew Choo (Malaysian women?s singles player) also did not feel well," he told Malaysian media.
"I am always careful of the food whenever I go for competitions. But we had no choice because it was difficult to get food if we returned late to the hotel.
"We even had to buy water from outside and that was only possible if the bus stopped at a mini-market on the way back.
"I hope the conditions improve when we return for the world championships. I will not be surprised if some of the players chose not to go."
Lee, who was runner-up at the All-England championships earlier this month and won the Swiss Open last week, also slammed the Indian officials who umpired his match against China's Chen Long.
"The umpires are not fit for a tournament of this standard, they need to improve their quality of judgement," said Lee, who was named Malaysia's national Sportsman of the Year this week.
"I hope it will be better in August."
The world championships have already been hit by controversy with delays in renovation work being carried out at the Siri Fort Sports Complex in New Delhi, forcing the tournament to be moved to Hyderabad.
The row is another blow to India's sporting reputation after cricket's showpiece Indian Premier League was moved to South Africa this week over security concerns in only its second year.