Mr Kennedy, who was forced to stand down as party leader two years ago over his alcoholism, was due to take part in Friday night's edition of Radio 4's Any Questions.
But at the start of the programme, broadcast from Brereton, near Stafford, host Jonathan Dimbleby announced Mr Kennedy would not be taking part.
He said: "Charles Kennedy was to have been the fourth member of our panel. However, he didn't make it. For one reason or another, he missed his train at Euston.
"We then made every effort to let him do the programme from London.
"But one way or another, he didn't turn up. He's gone off our radar."
Mr Dimbleby added that "mercifully, at the very last moment", Liberal Democrat chief executive Lord Rennard had been drafted in as a replacement.
The peer was on a train to London after campaigning in the nearby Crewe and Nantwich by-election. He had to disembark at Stafford to take part in the programme – even though he was going down with a cold.
Mr Kennedy's missed train will revive memories of an incident in the last few months of his leadership in 2005 when he abandoned a visit to Newcastle-upon-Tyne en route, although aides insisted at the time that a family illness was the reason.
Friends of the former party leader admitted last night that the latest incident would spark speculation over whether Mr Kennedy was still struggling to give up alcohol.
But Lord Rennard said: "As far as I know, it was absolutely nothing to do with drink. I saw him last Wednesday and he was in good form."
A former close aide of Mr Kennedy said: "I suspect that he just missed the train but the trouble is, his reputation goes before him.
"Nowadays, he does not have somebody with him all the time as he did when he was leader to remind him of appointments.
"I know someone who saw him on Thursday at lunch and who told me what fine shape he was in."
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