Igor Reshetin, director of TsNIIMASH-Export, is being held in Moscow's Lefortovo prison, along with his deputy and another top assistant.
Mr Reshetin is also accused of stealing 30m roubles ($1m; £597,000) through a scheme involving bogus companies.
TsNIIMASH-Export carries out research for Russia's state space agency.
The FSB said Mr Reshetin was charged with illegally selling technology that could have been converted for military use.
The recipient was named as a Chinese precision engineering import-export company.
The FSB did not release details of the technology transferred. TsNIIMASH-Export, established in 1991, is based in Korolyov - a space industry centre near Moscow.
'Public knowledge'
Last month, China completed its second manned space mission, thanks in part to Russian space technology.
Some rights groups say the FSB often interprets commercial activity as espionage, Reuters reports.
Last year, Russian physicist Valentin Danilov, 53, was convicted of spying for China and jailed for 14 years by a court in Siberia.
A few months before that judgement, weapons expert Igor Sutyagin was given a 15-year sentence after being found guilty of passing information to a UK firm that was allegedly a front for the CIA.
Both men proclaimed their innocence and said their work was all based on publicly available sources.
Rights groups have also raised concerns that the increase in convictions marks a return to Soviet-style scare tactics.
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