JAIPUR, INDIA — In a modern, air-conditioned office away from the dusty roads where honking cars and motorbikes swerve around camel-driven carts, Gagan Choudhary squinted at an emerald through a spectroscope: like most of the green stones sent to his laboratory these days, it would turn out to be not quite what it seemed.

“It’s like detective work,” he said. “Every stone is different. Some are so sophisticated that in some cases we spend at least two hours on an emerald.”

As deputy director and head tester at Gem Testing Laboratory in Jaipur, Mr. Choudhary sifts through thousands of colored stones each year, determining whether they are natural, laboratory-created, or treated with resin and injected with color to give a false brilliance.

The outcome: Nearly 95 percent of the emeralds, 99 percent of rubies and at least half of the sapphires tested these days are, in one way or another, unnatural, he said in an interview.