The limousines, valued at tens of million pounds, were part of a collection held at a military transport museum in the city of Ryazan, south of Moscow. They were supposedly transferred to state garages in the elite Rublevka suburb of the capital after then defence minister Anatoly Serdyukov closed the museum in 2010. However it is now thought that some of the machines went missing along the way and were sold off to private buyers.
The FSB apparently came across the suspected theft as part of a wider investigation into corruption at the defence ministry which led to Mr Serdyukov's sacking earlier this month.
President Vladimir Putin has said he removed the minister in order to ensure a transparent investigation into claims that employees of Oboronservis, a defence agency once headed by Mr Serdyukov, rigged privatisations of military real estate.
Russia's Ryazan museum was opened in 1994 to coincide with the 50th anniversary the following year of Soviet victory in the Second World War. Its collection included Soviet general secretary Khrushchev's six-litre ZIS-110 – worth up to GBP500,000 – and the ZiL-117 in which Cuban leader Castro was escorted during his visit to the Soviet Union in 1972.
Also kept there was the ZiL-111 cabriolet in which cosmonaut Gagarin was triumphantly delivered to Red Square after he became the first man in space in 1961.
The ZiL factory was in the news last month because it produced a luxury new machine for Mr Putin after years of gathering dust.
The Izvestiya newspaper claimed that Mr Serdyukov took a particular interest in the Ryazan collection soon after his appointment five years ago.
"Having found out that we had rare cars, Serdyukov gave an order to prepare him several photo-albums of all the exhibits, and photograph them from all angles," the museum's former director Rudolf Vander, was quoted as saying.
At a later visit to the museum, Mr Serdyukov was said to be accompanied by a young woman who nudged him and said, "We don't have a car like that" when they passed the famous models. "After that, the museum's problems started," said Mr Vander.
However, the timing of the investigation into the "limos affair" raised some questions. There has been a determined campaign to discredit Mr Serdyukov in state-linked media. Some commentators have suggested he fell victim to the Oboronservis probe because of his alleged extramarital affair with a young woman who is one of the suspects in the case.
Mr Serdyukov's father-in-law is Viktor Zubkov, the powerful chairman of the Gazprom state energy giant and an ally of Mr Putin. Mr Zubkov is thought to be unhappy with how the ex defence minister treated his daughter.