Such a measure would "actually be very problematic," Mitterlehner said at a news conference on Friday following a party meeting on the issue.
"It really is the last resort," said the chairman during the discussion, adding that he hoped those governors considering such a proposal would also see this.
"Ultimately border controls would damage Austria's international reputation," he said, describing the statements as a "cry for help to draw attention to the need for a quota system."
Austrian authorities have stopped 4,700 asylum seekers from entering Austria, most of whom had had their requests for asylum rejected in Italy.
Interior Minister, Johanna Mikl-Leitner views the current discussion similarly.
No one wants to "throw up borders", she said during the party meeting. What is important now is to find a European solution to the issue of quotas.
Meanwhile, the EU is discussing the possibility of setting up registration posts in North Africa, to try to stem some of the flood of refugees making the perilous crossing to Italy.
In Germany, the Bavarian CSU party is proposing the reintroduction of border controls between Germany and Austria, again due to the refugee issue.