<?php

$json = '{
  "origem": [
    {
      "id": 154826,
      "nm": "",
      "tp": "",
      "am": "",
      "sg": "SAO",
      "sq": 925
    },
    {
      "id": 2289,
      "nm": "",
      "tp": "",
      "am": "",
      "sg": "RIO",
      "sq": 925
    },
    {
      "id": 154826,
      "nm": "",
      "tp": "",
      "am": "",
      "sg": "SAO",
      "sq": 925
    }
  ]
}';

$rs = (json_decode($json, true));
$r0 = array();
foreach($rs['origem'] as $r)
{
    $r0[$r["id"]] = $r;    	
}

echo json_encode(array_values($r0), JSON_PRETTY_PRINT);