Pompey were relegated to the Championship after being deducted nine points for going into administration last season amid £135m of debts.
The Bluebirds owe an estimated £30m and are under new ownership.
"Have I any sympathy?, I was asked, and no, none whatsoever," said ex-Southampton manager Jones.
"Nobody's got any for us so why should I have any for them?"
Jones also says the Bluebirds "owe" Pompey a defeat after their 1-0 FA Cup final loss to them at Wembley in 2008.
Jones continued: "The easy option is go to into administration. But the option, sometimes, is taken out of your hands and clubs have to go into administration.
"This club had two decisions - do they or don't they? And they didn't and that's not a bad way.
"It means that we're paying down our debts bit by bit and everyone's going to get paid.
"I'm not saying that Pompey couldn't go into administration or whatever - maybe that's just the way it had to be for them.
"Lots of businesses do that and you can't get out of that. But our club decided not to and we got mullered from pillar to post because of that.
"But they've got their problems and we've got ours and we're trying to resolve ours just as much as they are and that's the way it is.
"And Stevie's [Steve Cotterill, Portsmouth boss] my mate - have I any sympathy?, I was asked, and no, none whatsoever because nobody's got any for us so why should I have any for them?"