Sir Brian Souter, a co-founder of the Stagecoach transport empire, is a friend and former political ally of Mr Salmond, donating more than £2m to the Nationalists before 2014.
The former First Minister has been charged with multiple accounts of sexual assault and two of attempted rape. Mr Salmond denies the allegations.
Sir Brian was speaking to worshippers at the Destiny Church in Glasgow when he referred to the case, The Times reported.
“Have you ever been really disappointed with someone that you really held in high regard?” he reportedly asked parishioners.
“I met with Alex Salmond at the airport a few months ago. I know him quite well and I like Alec. I’m not a fairweather friend. We had a good chat about things.”
He added: “I can’t tell you whether this (the court case) is right. I hope he gets justice and I hope his alleged victims get justice too. I can’t say anything about that but I would say this to you: I was disappointed, just that there’s a situation at all.”
Sir Brian has not made any donations to the SNP since Nicola Sturgeon became party leader in the wake of the 2014 referendum on independence.
Mr Salmond was charged with nine charges of sexual assault, two of attempted rape, two of indecent assault and one of breach of peace when he appeared at Edinburgh Sheriff Court in January.
He entered no plea during the hearing. After leaving court, he read a short statement to reporters. “The only thing I can say is I refute absolutely these allegations of criminality and I will defend myself to the utmost in court”.