KIEV—Ukraine intelligence officials said they knew three days before the downing of Malaysia Airlines Flight 17 that rebels in the east of the country possessed sophisticated air-defense systems capable of felling a jetliner at altitudes in excess of where the Boeing 777 was flying.

The disclosure deepens the mystery of why Ukrainian aviation officials failed to entirely close off the airspace in the Donetsk region, where the jet was flying went it was shot down, killing all 298 people on board.

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