Neeraj could not hurl the iron spear to the the automatic final round qualification mark of 83m in his three attempts with his best effort of 82.26m coming in his opening throw.
The 19-year-old world junior record holder then fouled his second attempt before clearing only 80.54m in his third and final throw at the Olympic Stadium here.
Five throwers, including world season leader Johannes Vetter (91.20m today) of Germany, came up with automatic qualification throws while Hamish Peacock of Australia was ahead of Neeraj at sixth spot in Group A with a best throw of 82.46m.
All the throwers who clear 83m or at least 12 best performers will make it to the final round to be held on August 12.
"I tried my best but I could not clear the automatic qualification mark of 83m and I am disappointed. I gave a lot of effort in the first throw but it missed the 83m mark by a few centimetres. There were some problems in the second throw and the third one also did not go the distance (of 83m). I have been training hard for this World Championships but I could not do well in the actual competition," Chopra said after his event.