This is the latest in a string of accusations of spying traded between the two countries.
Furqat Tuigunov, who was arrested by the Uzbek National Security Service, has reportedly admitted to being hired by the Tajik Security Ministry to conduct secret missions and assassinate "certain individuals" in Uzbekistan.
An Uzbek government website did not give further details.
Last month, Uzbek authorities detained another alleged Tajik spy whom they said was planning assassinations and terrorist attacks in Uzbekistan. Also in June, Tajik courts found two Uzbeks guilty of espionage, sentencing each to 13 years in jail.