Speaking to reporters in Jerusalem, Police Commissioner Yohanan Danino said a group of "extreme elements" were attempting "to create pressure and the impression of pressure" ahead of the pontiff's visit, which begins on May 25.
"There have been attempts here - principally as we get closer to the visit itself - by some extremists to try and make a provocation, and create a bad atmosphere before the visit," he said.
"We have absolutely no intention of tolerating this," he said.
Although police have made scores of arrests, there have been no successful prosecutions, prompting widespread expressions of concern from Christian leaders.
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"We will do everything to ensure they won't harm Christian holy places... And to ensure the trip goes successfully," said Danino.
He said there had been "no concrete information" about threats to the papal pilgrimage but that police were "not taking any chances".
Last week, Latin Patriarch Fuad Twal, head of the Roman Catholic church in the Holy Land, warned that hate crimes targeting Muslims and Christians was poisoning the atmosphere ahead of the pope's visit, with church officials "very concerned" about the lack of security.
"We know that this happens but we should not over-estimate them, or give them more importance than they have, because we know that the majority of the Israeli people are happy that the Holy Father is coming," he told reporters.