The Croatian police detained several Slovene nationals at the Plovanija border crossing point on Wednesday as they were on their way back from the village of Mlini where they visited Josko Joras, an ethnic Slovene who does not recognise Croatian sovereignty in that area.
Croatian journalists asked Sanader, who is in New York attending the annual UN General Assembly session, to comment on the incident.
Asked about his government's tolerance threshold with regard to such incidents from the Slovene side, the prime minister said: "Well, there is no tolerance. If someone violates the border, if they enter Croatia without documents and do not respect Croatian laws, then the Croatian police will act like in any other case."
Sanader said he was still awaiting a full report from the Croatian Interior Minister, but warned that "any kind of escalation will certainly not be good".
He said that this "act of provocation" from the Slovene side was motivated by the forthcoming elections, which are due to take place on October 3.
"We know that there are outstanding border issues between Croatia and Slovenia. But I am against any moves that might escalate those issues. If we cannot resolve them in bilateral negotiations to the satisfaction of both sides, then we should do what any other two countries would do, request international arbitration. That is what Croatia is proposing," Sanader said.
Sanader said that he hoped the situation would calm down after the parliamentary elections in Slovenia.
He, however, stressed that the border problem would remain unresolved. "We must resolve this problem either by bilateral agreement or by international arbitration," Sanader said.