Acting on the orders of an EU prosecutor, police arrested Hashim Rexhepi as part of a probe into corruption, tax evasion and money-laundering, the EU's rule of law mission (EULEX) said.
The first and only central bank governor since Kosovo declared independence from Serbia in 2008 is the highest ranking official arrested since EULEX launched several probes into misuse of public funds by high-ranking officials, including members of Prime Minister Hashim Thaci's cabinet.
Early Friday, EULEX carried out searches of the central bank offices and residences of four suspects, including the governor.
The arrest, confirmed by local police, came one day after the UN's highest court said that Kosovo's declaration of independence was legal.
Observers said the timing was a clear sign by the international community to Kosovo authorities to clamp down on corruption and strengthen the rule of law.
"The arrest means that EULEX will continue to strengthen robustly the rule of law area and will not avoid even high ranking probes," EULEX spokeswoman Karin Limdal said.