France's Manuel Valls and Hans-Peter Friedrich of Germany said Brussels had to increase aid to the two nations to stop the phenomenon, which was stretching the resources of their countries.
"Our two countries have been subject to a worrisome trend: a flood of asylum seekers from countries which have recently benefited from an easing of visa rules," Valls told France's Le Figaro and German newspaper Frankfurter Allgemeine Zeitung.
"Their nationals can move in the Schengen zone freely. This rush of asylum demands, often groundless, is threatening our system," he said, when asked specifically about Bosnians and Macedonians.
Macedonia, Montenegro and Serbia were granted visa-free status by the European Union in December 2009, thereby allowing their citizens to travel unhampered in the passport-free Schengen zone.
Valls complained that domestic laws forced the two countries – the economic heavyweights of the eurozone – to house and feed the asylum seekers "even though it's almost sure that their demand will be rejected."
"This problem should be met with a European response," he said.
Friedrich said the European Union "could offer Serbia and Macedonia adequate aid."
He said if this did not resolve the problem, the visa-free travel would be lifted in line with decisions taken in the European Council.
"There, that's our message to Serbia and Macedonia. We are asking these two countries to resolve the problem."
In a separate interview on German broadcaster ARD, Friedrich said the two nations had to better integrate their sizeable Roma population into the mainstream.
"If they want to belong to Europe, they must cooperate on who ultimately takes care of these people," he said. "They have to do things so that these people … don't feel discriminated against."
Several EU nations, especially Sweden, Belgium and Germany have been swamped by asylum seekers from Balkan countries in recent years.