OP Jaisha said she "could have died" after the women's marathon in Rio.
Jaisha, 33, finished in 89th place and collapsed after finishing the 42km (26 miles) race in two hours 47 minutes 19 seconds last week.
Indian officials denied the allegation and said Jaisha and her coach had refused refreshments.
The Athletics Federation of India (AFI) said officials in Rio were not told by the athletes or their coaches about any specific requirement for any drinks.
"It is the responsibility of the organisers to provide water and energy drinks. For that there are water and energy stations throughout the course," senior AFI official CK Valson told the Press Trust of India (PTI) news agency.
"We could have provided water and energy drinks to our athletes but neither they nor their coaches informed us that they would need water and energy drinks separately."
Jaisha said she ran "in scorching heat" and there was no water available from Indian officials during the race.
"Only once in 8km did we get water [from the Rio organisers] which did not help at all. All the countries had their stalls at every 2km but our country's stall was empty," she was quoted as saying by PTI.
Jaisha had to be taken to hospital after finishing the race.
"We are supposed to be given drinks by our technical officials, it's the rule. We cannot take water from any other team. I saw the Indian board there but there was nothing," she said.
"I had a lot of problem, I fainted after the race. I was administered glucose, I thought I would die."
Jaisha said she got no response from officials when she asked why water was not provided to her at the stalls.
"I don't know who to blame for this. May be nobody realises the seriousness of a marathon, the fact that we  have to run 42km," she said.
India's Sports Minister Vijay Goel has said he will investigate the allegation.
"I'll look into this and if there was negligence of any sort, action will be taken," he told NDTV.
India finished with just two medals at the Rio Games, fewer than the six medals it won during its best-ever performance in London four years ago.
An Olympic woman marathon runner from India has alleged she was not provided water and energy drinks by Indian officials at designated stations.