Junior Hoilett clawed one back four minutes into the second half but Southampton ensured a 3-1 victory courtesy of a late Anton Ferdinand own goal, leaving the Rs without a win this season and their manager under increasing pressure.
Asked if it was the worst QPR performance of his time in charge, Hughes said, "Yes, without a shadow of a doubt.
"Today there was not that intensity. We weren't on the front foot, we weren't anticipating anything, we weren't aggressive enough. All the fundamentals that you need to build a performance [were not there].
"Maybe the anxiety of the significance of the game filtered through to them but, come on, the vast majority of them are very experienced.
"It shouldn't affect them in that manner and it surprised me that possibly it did.
"I can well understand the reaction [from the fans]. In fairness, it was exactly my reaction to that performance.
"We are not going to hide or try to make it positive out of a very big negative because it was a huge game for everybody connect with Queens Park Rangers, including myself, players, staff and fans.
"We have not performed, unfortunately, so when that happens it puts us in a situation that no-one anticipated this year but we are where we are."