The Fast Show's Charlie Higson recently suggested that the format has taken over from sketch shows because they are "much cheaper to do".
His colleague John Thomson added: "These shows are produced by agencies who have their acts, and only their acts on those shows and it's not opened to everybody.
"It's a closed shop, which isn't right. That's why you see the same faces appearing on panel games."
In response, Flanagan told Digital Spy: "I think things have their moment - they come in waves. The sketch comedy wave was big and made a lot of people's careers, and made a lot of people very, very wealthy, and I think they should be pleased about that.
"I get a little bit worried when comics start saying that one thing is spoiling it for everyone else. If you think panel shows are genuinely spoiling comedy or making it hard - produce a really good sketch show, and you'll be surprised at how many TV companies jump on it."
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Of the "closed shop" claims, he added: "It's not an accident that certain comedy agencies have a lot of great comics on their books.
"If a producer goes to them, 'I'm producing this new panel show, can I have Sean Lock or any decent comic?' they're told, 'Yeah, you can - you know we've also got...'
"The reason all those acts come from that single company is because that company gets all the best, talented acts because it looks after them the best."
> Read Digital Spy's full interview with Micky Flanagan