Al Fayed, a close friend of the late performer, has caused controversy after announcing he had decided to place the tribute to Jackson outside the Cottagers' stadium.
The statue was commissioned following Jackson's death in June 2009 and was due to be erected at Harrods before Al Fayed sold the Knightsbridge store.
Was it a Thriller? Jackson visited Fulham with Al Fayed in 1999
The decision to relocate it to Craven Cottage is likely to divide opinion, with statues at football grounds generally reserved for club legends.
Jackson's links to Fulham are tenuous to say the least - he watched a game there as a guest of Al Fayed in 1999 - while the singer was also dogged by controversy during his lifetime.
But Cottagers boss Hughes refused to criticise Al Fayed, saying: 'In fairness to the chairman, he's fully supported this club for a long time now, put in something like ?200million.
'And if he wants to make that gesture to somebody who he knew personally then who am I to pass comment on it.
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'What has to be judged are the reasons behind it. And the reasons are he was a close personal friend of the chairman of Fulham Football Club, and he obviously wants to mark that and make people understand the respect and affection that he had for the guy.'
Hughes, who revealed he was a fan of Jackson's music, acknowledged the move would be controversial.
'The fact that it's at the football club will maybe cause a debate,' he said. 'But, really, we shouldn't question our chairman's motives.'
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Explore more:People: Mohamed Al Fayed, Mark Hughes, Michael Jackson Organisations: Fulham Football Club