Angry fans initially pointed the finger at Apple for the increase in price of Houston's greatest hits album, The Ultimate Collection, from £4.99 to £7.99.
However, The Guardian reports that it was actually record label Sony Music which increased the album's wholesale price at about 4am California time on Sunday.
Originally released in 1997, The Ultimate Collection was the second biggest-selling album on iTunes on Monday, after Apple returned the record to its original price late yesterday.
But fans of the singer have hit out at the temporary price increase as it came so close to the 48-year-old being found dead at the Beverly Hills Hilton on Saturday afternoon, local time.
Some described the move as "cashing in" on the tragic death, while others said that Apple and Sony Music should be "ashamed" of the alleged "shameless exploitation".
One customer was quoted as saying: "To say I am angry is an understatement and I feel it is just a case of iTunes cashing in on the singer's death, which in my opinion is totally parasitic.
"The album itself is great so please don't be put off purchasing it, just [realise] that you will merely be lining some fatcat's pocket before Whitney's lifeless body is cold."
Sony Music, which owns the rights to the majority of Houston's back catalogue, is thought to have increased the wholesale price of The Ultimate Collection, causing Apple to automatically boost the price on iTunes.
The Guardian claims that Sony Music opted to review Houston's entire iTunes catalogue after the singer was pronounced dead.
An insider told the paper that the album's price increase was not a "cynical" move, but admitted that the wholesale cost for The Ultimate Collection had been wrong.
Apple and Sony Music declined to comment.
View a gallery of Whitney's music achievements below: