Rangers sources suggested on Saturday morning their west London rivals had accepted a bid for the wantaway Brazilian but the Blues later insisted that was not the case.
QPR had an offer rejected earlier this week but reportedly returned with an increased bid they appeared to believe would allow them begin discussing personal terms with the 29-year-old.
However, a Chelsea spokesman said: "I can say at this time there is no agreement between the clubs."
Manager Andre Villas-Boas added: "I'm sure that the clubs can reach an agreement if they continue to push.
"We know Alex's market value and we're just not going to let him go quite easily, not that QPR's offer is far, far off.
"He is a player that has attracted a lot of interest from Premier League clubs and from abroad."
Even if a fee is agreed, convincing Alex to join QPR is far from a formality amid reports he may no longer wish to remain in England.
Alex, who has also been linked with Paris St Germain and Juventus, was banished from Chelsea's first-team squad in November after submitting a transfer request.
His signing would represent another coup for ambitious Rangers after they convinced Hughes to succeed Neil Warnock as manager on Tuesday.
As well as having a previous bid for Alex snubbed - reportedly £3million - they have had offers turned down for Andy Johnson, Christopher Samba, and yesterday Steven Pienaar.
Should Rangers complete Alex's signing, he would have to wait to make his debut as the club missed the deadline for tomorrow's Barclays Premier League game at Newcastle, while he is ineligible for Tuesday's FA Cup third-round replay against MK Dons.
His first game could therefore be next Saturday's league match against Wigan, which is followed by a possible FA Cup clash with Chelsea.
Speaking on Wednesday, Hughes said of Alex: "There is interest in top-quality players and the player you mention is very much in that level."
Chelsea signed Alex from Santos in 2004 but work-permit issues saw him loaned to PSV Eindhoven for three seasons before he joined his parent club in the summer of 2007.
The Brazil international helped the club win the FA Cup in 2009 and their first ever double the following season.
The arrival of David Luiz a year ago saw him marginalised and although he eventually won back his place and started this season in the team, he soon fell back behind Luiz in the pecking order, culminating in his transfer request.