The Canaries boss admitted that his team should have won the game against such lowly opposition, but paid credit to Paul Buckle's men.
"It is a big shock," said Hughton. "We were rightly expected to beat them and this will be a tough few days. We have to give Luton credit. They came with a gameplan and they relied on a few things happening to get the result.
"We found it very difficult to break them down. The good chances we had we could not put them away and that would have changed the game. Even in the second half period when we pushed and pushed they caught us on the classic counter-attack.
"We wanted to push but we knew these were a fit side. Perhaps that one opportunity they had they scored in the second half."
Norwich play host to Tottenham Hotspur in the Premier League on Wednesday.