Clint Hill thought he had given the visitors the lead in the 19th minute when his header from Joey Barton's corner clearly crossed the line before it was clawed out by Adam Bogdan, but neither referee Martin Atkinson nor his assistant gave it.
Darren Pratley then opened the scoring for Bolton in the 37th minute and, although Djibril Cisse equalised just after half-time with a goal that was shown to be offside, Ivan Klasnic netted the winner four minutes from time to lift Bolton above their opponents and out of the relegation zone.
The FA released a statement during the match reiterating their "strong desire to see goal-line technology introduced as soon as possible", but Hughes was not impressed by the timing.
The QPR boss said: "The laughable thing is the FA have come out and said they're all for goal-line technology. I think that's absolutely ludicrous that they come out and try to protect the poor performances of the officials they supply us. It's a joke."
Regarding the display of Atkinson and his assistants, Hughes said: "All you ask for is the key decisions in games to be judged correctly and I felt that wasn't the case all day.
"Martin Atkinson's acknowledged as one of the better referees and his performance was okay but I thought he was let down by his assistants.
"Obviously from our point of view to have that clear goal chalked off was a significant moment. Don't underestimate the significance of scoring first. We're the away side, we're at the wrong end of the table and to score first is crucial for us.
"If we scored then I think we would have taken the game away from Bolton because they would have had to come out and try to get back into the game. Not getting a decision of that magnitude correct impacts on what we feel we can get out of the game.
"In fairness they even got our goal wrong because that was slightly offside so they haven't covered themselves in glory. They missed a penalty, they missed a handball in the area. In the end I think the guy on my side completely lost his nerve to make any decisions."
FIFA, football's governing body, have so far resisted goal-line technology as well as other proposed ideas such as instant replay and adding extra officials.
However, following Frank Lampard's disallowed goal in the 2010 World Cup, FIFA president Sepp Blatter hinted that technology could be in place in time for the 2014 World Cup in Brazil.
The Premier League are investigating whether it is feasible to bring in goal-line technology for next season ahead of a July decision by football's law-makers.
The International FA Board (IFAB) have approved goal-line technology in principle and will go ahead with final tests on two systems, one from British company HawkEye and GoalRef by a German-Danish firm.
A final decision will be taken in July and, even though the new season kicks off only six weeks later, Premier League sources say they will look at whether it could be possible to have a system in place.
Despite his anger, Hughes and Bolton counterpart Owen Coyle are both strong supporters of technology being introduced into the game.
Hughes said: "It should come in, but until it comes in then the assistants should do the job they're supposed to, which is check whether the ball has crossed the line."
Coyle added: "Nobody's a bigger advocate than myself of goal technology. You've seen what happened to England at the World Cup, that game could have been totally different against Germany. But it obviously has to be a fool-proof system that comes in.
"I know the argument from FIFA that it can't happen in football worldwide, but when you play at our level and the top leagues in Europe then I think it's got to come in because the difference (these decisions) make to clubs could be huge."
Meanwhile Coyle praised the patience of match winner Klasnic, who has mostly had to make do with a place on the bench this season despite netting nine times this season.
He came off the bench again in the 80th minute and needed only six minutes to make it 2-1, taking Ryo Miyaichi's clever pass before slotting coolly past Paddy Kenny.
"Of course it's been frustrating for Ivan not to play because he's our top goalscorer, but equally when we were scoring goals we were conceding far too many as well, so we had to do something about it," Coyle said.
"The extra man in midfield brought some good results and David Ngog has been outstanding for us. Ivan's had to be patient but he showed what he's got to offer today [Saturday] and it's a wonderful goal."
Coyle added: "It's such a valuable three points. I said in the build-up that it was our biggest game of the season, playing against another one of the five teams in our group - we have to finish first or second in that group.
"We scored two great goals, there were so many incidents in the game. Clearly Queens Park Rangers scored in the first half with the ball over the line.
"Having said that it was a wonderful knock out from Adam Bogdan to keep it alive, although it was clearly a goal.
"Our disappointment is that QPR's goal is clearly offside. I'm sure Mark won't feel it evened itself out because they would have been in front.
"They've got sublime quality but our lads stood up brilliantly to that and I felt in the last 15 minutes it was a game we could win.
"We sent on another striker in the shape of Ivan Klasnic and it could not have worked out any better. When Ivan goes one-on-one with the goalkeeper, there's normally only one result."
The result left Rangers in big trouble ahead of a run-in that includes games against all the Premier League's so-called big six, and Hughes was left with a feeling of injustice.
He said: "We came here with a positive attitude, we tried to take the game to Bolton because when you're at the bottom draws don't really move you, you need to win games.
"We had two up front and we deserved something out of the game. All we hope for is a level playing field. If we get beaten fairly and squarely then we'll hold our hands up but that's not happening at the moment."