Arabs, who make up a fifth of Israel's population, and Palestinians living in Israel have long complained of being singled out for scrutiny and searches at security checkpoints when going about their routine activities.
Trump, the Republican front-runner who has been buoyed by Americans' worries about Islamic militancy, said on Sunday he believed that "profiling is something that we're going to have to start thinking about as a country."
"You look at Israel and you look at others, and they do it and they do it successfully," he told CBS' "Face the Nation."
Asked about the remarks, Israeli Transportation and Intelligence Minister Yisrael Katz declined to discuss the US election campaign but was unapologetic about Israel's methods.
"Ultimately these (security) apparatuses ... must build a profile of characteristics as to where the danger comes from and locate it," he said in a briefing to foreign journalists arranged by the Israel Project advocacy group."It is not the whole population, but sometimes when there is a specific form of terrorism, you can seek out Islamic terrorism only among Muslims."