The tricolour was hoisted last month but keeps getting torn by the wind and is being replaced for a fourth time.
It was launched with media fanfare but now officials say national pride is being dented and money wasted.
Pakistanis are likely to be amused - the aim was for the flag to be seen from deep inside their territory.
Indian press reports at the time said the 106m (350ft)-tall flag at the Wagah crossing would be visible from Lahore, 20km (12.5 miles) away.
Instead, officials have had to spend more money on replacements because by law a damaged flag cannot be flown.
Suresh Mahajan, the chairman of the Amritsar Improvement Trust, which is responsible for maintaining the flag, said that the situation amounted to a "crime".
"The national flag is our pride and I request the government to call an inquiry over the issue and those responsible should be punished," he told BBC Hindi.
Gurpreet Singh Soni, who runs a shop at the border, said the absence of the flag was "disappointing" visitors.
Apparently, Indian planners didn't take into account the strong winds the Wagah flag would face.
The chief of the Flag Foundation of India, KV Singh, said he had advised against such a tall flag.
"We had suggested to hoist a smaller flag to avoid frequent damage but the aim is to ensure that the Indian flag is visible from Lahore in Pakistan."
The Wagah flag is not the only Indian one to face problems.
An 88m flag in the southern city of Hyderabad installed near the 455-year-old Hussainsagar lake also keeps tearing because of strong winds.
And KV Singh said a 63m flag in the capital, Delhi, tore 11 times in May and June last year.
"This despite the Delhi flag being a smaller flag than the one in Hyderabad. So damage is normal when the flag is high," says Mr Singh.
India's tallest flag, which towers over the border with arch-rival Pakistan, is causing red faces - because it cannot stand up to the weather.