The FSB was quoted as saying that the men are brothers with the family name Zaslavsky.
Russian agencies said the men hold US and Russian citizenship..
Industrial espionage is punishable by up to two years in jail.
TNK-BP, a joint venture with British oil company BP and Russian investors, said on Thursday that it had not engaged in any illegal activity.
"TNK-BP is a Russian company. We operate on Russian soil and we operate always within the framework of Russian legislation," a company statement said.
"We have never countenanced or supported any actions which try and counter Russian legislation or fair business practice."
A spokesman for the British embassy in Moscow said: "We are aware of the events. We are monitoring the situation closely and we are in touch with BP."
The arrests came after raids on Wednesday by security officers and police on the headquarters of BP and TNK-BP.
During the searches security forces found the "business cards of representatives of foreign defence departments and the [US] Central Intelligence Agency," Interfax quoted an FSB statement as saying.
It is not clear whether either of the men are believed to have foreign intelligence connections.
The raids recalled similar actions in 2003 against the Yukos oil company, which eventually collapsed.
TNK-BP has already been investigated by the FSB for alleged breaches of Russian legislation on state secrets.
There is little confidence that foreign investors in Russia's oil and gas sector receive adequate protection following official campaigns in the past years which have forced Shell and BP to sell assets to groups close to the Kremlin.
Relations between Britain and Russia, already tense since the 2006 poisoning murder of a former Russian agent in London, could deteriorate further in the wake of Thursday's arrests.
Russia has refused to extradite Andrei Lugovoi, the man identified by Britain as the main suspect in the killing of Alexander Litvinenko.
Both countries have expelled some of the others' diplomats, while Russia has also closed the St. Petersburg and Yekaterinburg offices of the British Council, a cultural organisation within the British government.