The study found that more than half of the men measured had penises that were shorter than international standards for condoms.
It has led to a call for condoms of mixed sizes to be made more widely available in India.
The two-year study was carried out by the Indian Council of Medical Research.
Over 1,200 volunteers from the length and breadth of the country had their penises measured precisely, down to the last millimetre.
The scientists even checked their sample was representative of India as a whole in terms of class, religion and urban and rural dwellers.
The conclusion of all this scientific endeavour is that about 60% of Indian men have penises which are between three and five centimetres shorter than international standards used in condom manufacture.
Doctor Chander Puri, a specialist in reproductive health at the Indian Council of Medical Research, told the BBC there was an obvious need in India for custom-made condoms, as most of those currently on sale are too large.
The issue is serious because about one in every five times a condom is used in India it either falls off or tears, an extremely high failure rate.
And the country already has the highest number of HIV infections of any nation.
'Not a problem'
Mr Puri said that since Indians would be embarrassed about going to a chemist to ask for smaller condoms there should be vending machines dispensing different sizes all around the country.
"Smaller condoms are on sale in India. But there is a lack of awareness that different sizes are available. There is anxiety talking about the issue. And normally one feels shy to go to a chemist's shop and ask for a smaller size condom."
But Indian men need not be concerned about measuring up internationally according to Sunil Mehra, the former editor of the Indian version of the men's magazine Maxim.
"It's not size, it's what you do with it that matters," he said.
"From our population, the evidence is Indians are doing pretty well.
"With apologies to the poet Alexander Pope, you could say, for inches and centimetres, let fools contend."