The Hollywood film producer vehemently denied the rumours via Twitter this morning, calling them "disgusting and untrue."
Stephen spoke out after Mel's appearance on last night's X Factor finale, which came after she skipped the Saturday evening show due to an undisclosed illness.
Some fans on Twitter were quick to point out Mel was not wearing a wedding ring. Others claimed her face looked bruised.
But an angry Stephen has now responded, saying: "I don't usually respond to Twitter messages but I will respond to comments of hitting my wife which I think are quite disgusting and untrue!
"Mel was very ill. A bunch of doctors helped her get better. If fans can't just relax before being negative they are not real fans of Mel."
Former Spice Girl Mel is believed to have been taken to hospital on Thursday, ahead of a planned appearance at an X Factor press conference.
She is thought to have remained in hospital for three nights before being discharged on Sunday and given the all-clear to return to X Factor.
Mel has not disclosed details of her illness, only saying last night: "I really missed being here. Thanks to all the doctors and nurses who took care of me and got me here tonight."
While she appeared on X Factor last night, she did not appear on spinoff show Xtra Factor.
Mel recently spoke with Fabulous magazine about her marriage to Stephen, calling him her "rock" in life.
"He's my rock," she said. "When nobody believed in me, he was the one saying, 'You can do whatever you want'. I would like to say, 'It's all me, baby!' but he literally is my world."
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