Hughes attended a two-hour meeting with the club's chief executive Philip Beard on Monday and did not take charge of training.
That led to internet rumours that Hughes was about to be axed from his position and Sky Bet also suspended betting on Hughes being the next Premier League boss to get the chop.
Beard made no comment as he left Rangers' west London training ground on Monday afternoon.
But the club later told Sky Sports News it was "business as usual", while a source close to Hughes said that meetings on Monday are normal and that he is preparing as normal for Saturday's game against Manchester United.
QPR's head of media Ian Taylor also tweeted: "Rumours suggesting Mark Hughes has been sacked as QPR manager tonight are NOT true."
Pressure continues to mount on Hughes after Saturday's defeat to fellow Premier League strugglers Southampton left QPR rock-bottom of the table.
The Hoops are yet to win a game this season and have claimed just four points from their 12 matches so far.
QPR owner Tony Fernandes has, however, publicly backed Hughes on several occasions in recent weeks.
Fernandes, who is thought to have been in the United States on business, tweeted earlier on Monday: "On my way home from America. Long long flight to think of many things. Just stopped of at Osaka. Now back home to Kuala Lumpur."