The case has echoes of the old days of the KGB
"The mission was carried out by CIA officers, working under cover of US diplomatic representations in Moscow and one of the CIS countries," the FSB said in a statement.
The US embassy in Moscow has refused to comment on the case, which comes just weeks before a US-Russian summit.
Tricks of the trade
"The FSB has irrefutable evidence of the CIA's spying activities against Russia," an FSB official said.
A diplomat at the US embassy in Moscow is accused of leading an operation to recruit a Russian defence ministry specialist who was working on top secret matters.
She allegedly used coded letters, invisible ink and dead letter boxes to communicate with her target.
Another CIA undercover agent, a man named as David Robertson, is alleged to have met the informer outside Russia.
"The timely intervention of the Russian counter intelligence services enabled them to uncover the CIA's plans at an early stage, bring their activities under control and prevent serious damage to Russia's security," the FSB said.
Tensions rising
Russia and the United States have traded mutual accusations of spying a number of times in recent years.
Just over a year ago, the US expelled 50 Russian diplomats on spying charges, prompting Russia to expel 46 American diplomats, after FBI agent Robert Hanssen was revealed to have spied for Russia.
And six months before that, American Edmund Pope was sentenced to 20 years in jail for trying to acquire military secrets.
President Vladimir Putin later pardoned him on grounds of ill health.
The latest spying allegations are set to heighten tensions before Mr Putin meets US President George W Bush in a few weeks' time.
After a brief spell of detente, following the 11 September attacks, friction between the nations has recently grown as they come into conflict over issues including steel tariffs and poultry imports.