"The arrested man confessed that he intended to sell the plutonium to citizens of Afghanistan or Pakistan for 21,000 dollars," said Avaz Yuldashev, spokesman for the drug control agency in the Central Asian country.
Yuldashev did not release the suspect's name, but said he was a citizen of neighboring Uzbekistan.
"Tajik special services suspected him of drug smuggling, but during a search found a capsule of factory-grade plutonium that was likely made either in Russia or Kazakhstan."
Tajikistan is a main smuggling route for drugs destined for Western markets from Afghanistan, with which it shares a 1,340-kilometer (830-mile) border that is patrolled by thousands of Tajik and Russian troops.
The economic disarray that followed the breakup of the Soviet Union has sparked fears that downtrodden scientists would sell to extremists weapons of mass destruction from the former superpower.