"We are very critical of Denmark's decision to re-establish permanent customs checks at the border with Germany," he said after meeting Lene Espersen, who was in Berlin on what was billed as a fence-mending mission.
"We will continue our dialogue on the issue ... we must continue to discuss it," he told reporters, adding that he was pleased Espersen assured him that Denmark would not introduce passport checks at the border with Germany.
Espersen insisted that the new border checks were in full agreement with the Schengen accords governing the 26-nation passport-free area and that their aim was "to fight the entry of illegal goods and drugs" into Denmark.
"Denmark will remain a country open to the world," she said.
After Westerwelle, Espersen is to meet Swedish Foreign Minister Carl Bildt on Friday and Poland's Radoslav Sikorski Monday on the sidelines of a meeting of EU foreign ministers in a bid to cool tensions over the plan, her ministry said.
Denmark's centre-right government hammered out the customs plan under pressure from its far-right ally.
The move, which has met heavy criticism both at home and abroad, had been set to easily pass through Denmark's parliamentary finance committee last week.
But a counter-proposal by the opposition forced the government to put the matter to a full vote in parliament. No date has yet been set for that vote.
Critics at home and abroad, especially the European Commission and Germany, have cautioned that the plan would undermine the principles of the Schengen area.