Vlado Buckovski met with Kosovo counterpart Agim Ceku in Skopje to discuss the issue.
Kosovo is claiming some 2,000 hectares (5,000 acres) of Macedonian territory, from a 2001 border agreement between Skopje and Belgrade that Ceku recently said Pristina did not recognize.
Kosovo has been under U.N. administrative control since the end of the war between Serb forces and ethnic Albanian separatists in 1999.
A fifth round of U.N.-mediated talks between ethnic Albanian and Serbian officials on the larger dispute of the future of Kosovo is scheduled for May 23 in Vienna.
Buckovski said only technical questions remained with the Macedonia-Kosovo border, and not political ones, but did not elaborate.
"The demarcation of the border will be part of the final solution for Kosovo," he said.
In a statement issued late Thursday, the Kosovo government said it was "against any change of borders with its neighbors, including Macedonia."
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