Pristina on Monday advised its citizens not to use neighbouring Serbia as a transit country after the second arrest of a Kosovo Albanian in a month.
Serbian authorities on Friday arrested Hilmi Kelmendi, 36, as he was travelling from Kosovo to Germany on suspicion of committing war crimes during the 1998-1999 conflict, a statement from the foreign ministry in Pristina said.
It denounced the arrest as "unacceptable".
In Belgrade, an interior ministry official confirmed Kelmendi's arrest on the basis of a court warrant, saying he was currently "in hands of the war crimes prosecutor's office." She declined to provide further details.
At the end of September, Serbian police also arrested Nehat Thaqi, Kosovo police's director of the northern Mitrovica area, as he crossed into Serbia. He was detained on suspicion of "terrorism" although the specific allegations are unknown.
On Friday, a Belgrade court extended his one-month detention for another 30 days.
Following the arrests, Kosovo's foreign ministry urged all citizens to "who, for whatever reason, choose Serbia as a transit country, to avoid it as much as possible in the coming months."
"This arrest is unacceptable and endangers many processes achieved during the dialogue for the normalisation of relations between Kosovo and Serbia," the ministry said.
Since 2011, Kosovo and Serbia have been negotiating under EU auspices to improve ties which have remained strained since the end of the war and particularly since Pristina's unilaterally declaration of independence in 2008 that Belgrade refuses to accept.
Freedom of movement was one of the first accords clinched, and since December 2011 Serbia agreed to allow ethnic Albanians to travel across the "border/boundary" on the basis of ID cards.
The war between Serbian security forces and pro-independence ethnic Albanian guerrillas ended after a three-month NATO air campaign that ousted Belgrade-controlled troops from the breakaway province of Kosovo.
The war claimed some 13,000 lives, mostly ethnic Albanians.