Race organisers at Sunday's Indian Grand Prix could not use electronic timings due to a power cut at New Delhi's Jawaharlal Nehru Stadium.
Amiya Kumar Mallick was 0.07 seconds inside the Olympic men's 100m mark.
Srabani Nandaware was 0.09 inside the women's time but like Mallick must try again at the same venue this week.
Mallick, 23, was timed at 10.09 seconds, breaking the national record by 0.21 seconds and surpassing the Olympic qualification mark of 10.16 seconds.
Nandaware, 24, won the women's sprint in 11.23 seconds, breaking the 16-year-old national record by 0.15 seconds as she surpassed the Olympic qualification time.
"It's disappointing because I knew I had run a quick time. But it will not count for anything because the electronic timing was not working," Mallick told the Indian Express.
An official at the Athletics Federation of India, which organised the event, said stadium administrators are blaming the blackout on a transformer fire.
"There were generators there but still they said there is no back up," the official told AFP.
The athletes have another opportunity to qualify for this summer's Olympics in Rio at the Federation Cup, which will be held at the same venue from 28-30 April.
Two Indian sprinters must still qualify for Rio 2016 after their new national records were not ratified as a result of being recorded on hand-held clocks.