Most important, he is accused of doing this without state regulators certifying the changes.

It is a case that highlights the tensions between Mr. Putin’s aspirations for a dynamic private sector and his determination to enhance the powers of Russia’s security apparatus. Using a 2014 law meant to protect Russians from counterfeit medicine, investigators from the Federal Security Service, the post-Soviet KGB, and other agencies have accused Mr. Trubitsyn of leading a criminal conspiracy to, essentially, innovate too fast and too freely.

Image Dmitri Trubitsyn Credit... Natalia Zapechenko/Tion

The situation has outraged fellow scientists, would-be entrepreneurs and others in Akademgorodok, a freethinking settlement of broad avenues, forested pathways and 35 Soviet-era research institutes near the Siberian city of Novosibirsk. They see it as the Russian government undermining its own stated economic goal — to nurture enterprises that harness Russian brain power instead of sucking oil, gas and minerals out of the ground.

More than 5,000 people have signed a petition appealing to Mr. Putin to stop “this shameful example of forceful pressure on a law-abiding business.” Mr. Trubitsyn and his company “are, without exaggeration, the pride of Akademgorodok,” it said. “They are a strong symbol of a prospering Russia in which real technological business can develop to world standards.”

Aleksei Okunev of Novosibirsk State University in Akademgorodok, who has worked closely with Mr. Trubitsyn’s company, called the situation “incomprehensible.” He added, “We have very few success stories in Russia, and this explains why.”

Mr. Putin did not respond, but in a statement, his business ombudsman, Boris Titov, called Mr. Trubitsyn “a young, energetic representative of the innovation sector, the development of which is most needed for a modern Russia.”