Intelligence agencies "must characterise, see where the dangers are coming from, and locate them," Israeli Intelligence Minister Yisrael Katz said.
"It's not the entire population, but sometimes there is a certain type of terror such as Islamic terror. You can only look for it among Muslims," he said in a briefing to reporters.
Trump, the free-talking presumptive Republican presidential nominee, came close to endorsing profiling outright in an interview aired Sunday on CBS.
Trump was asked point-blank if he was talking about increasing profiling of Muslims in America.
"Well, I think profiling is something that we're going to have to start thinking about as a country," Trump told the programme "Face the Nation".
He added: "So we really have to look at profiling. We have to look at it seriously. And other countries do it, and it's not the worst thing to do. I hate the concept of profiling, but we have to use common sense."
Katz, who refused to address Trump's remarks directly or weigh in on the US elections, argued that the United States did in fact employ racial profiling in practice.
"The United States does it, they know how to act. At the end of the day, there's a war here... With a murderous ideology with very clear goals, that wants to topple Western civilisation," he said.
Speaking of Israel's internal security agency, Katz said "the Shin Bet acts based on assessments and evaluations pertaining to specific communities."
Israeli Arabs and Palestinians say they face abusive security measures, including in airports and at border crossings.
Katz, who is also transportation minister, said the world was seeking to learn from Israel's experience on airport security.
"It's a very sensitive topic, the threats are great, at the planes, at the airports. We collaborate on the issue and people come here to learn the Israeli practices."
A spokesman for Israel's Airport Authority denied the use of profiling at their facilities, stressing to AFP that "Israel conducts the same security checks to the luggage and bodies of all passengers.
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