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The EU has a program called "one-stop security", where some countries' aviation security practices are recognized as equivalent to EU standards, so passengers on flights arriving from those countries do not have to clear security again when connecting at an EU airport. Those countries are
However, implementation of this can in practice be mixed, and some passengers on some flights at some EU airports from some one-stop countries may be subject to security re-screening anyway.
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This is a requirement for US-inbound flights. DHS outlines this reasoning:
....Secretary of Homeland Security John Kelly has determined it is necessary to implement enhanced security measures for all commercial flights to the United States. These measures, both seen and unseen, include enhanced screening of passengers and electronic devices as well as heightened security standards for aircraft and airports.
Countries: 105 Airports: 280 (approximate number as it will vary based on seasonal airports) Total airlines: 180 Average daily flights: 2,100 Passengers: 325,000 average daily passengers
See the link here
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That's unfortunately normal. By default all connecting passengers have to go through security and plenty of airports do this for everyone regardless of where you come from (London (LHR), Paris (CDG), Doha (DOH), etc.)
Some airports can choose to skip security if the incoming flight is from a "good" country (which is determined by a variety of criteria). Frankfurt, Vienna, Tokyo Narita, etc. are examples of that.
You can never predict with certainty what's going to happen. We flew EWR<->CGK through Tokyo. On the outbound we just walked from the plane into the Terminal. On the return flight last week we had a totally different experience: First they deplaned all passengers that were entering Japan and held everyone else back on the plane. Only after this we were allowed to get off the plane only to be greeted by a very long security line. I'm fairly sure some people missed their connection that day. No idea why they did that.