The Westminster leader was also asked about the row over Scottish Health Secretary Neil Gray using a ministerial car to attend football games.
But he insisted it was "not a scandal".
Gray, whose portfolio includes sport, has been under fire after it emerged he had been chauffeured to six football matches at Hampden since becoming a minister, four of which included the team he supports.
The Aberdeen fan apologised last week in a ministerial statement and conceded he should have went to a "wider range" of football matches.
Flynn defended Gray and told The Sunday Show: "Our sports minister going to sporting events is not a scandal.
"He's doing his job and he's doing his job to the best of his ability."
He added: "What tends to happen in politics is you tend to create relationships, have discussions with people and that could only happen by being in those places at certain times.
"Neil is a huge sports fan, I think it's right that he, as sports minister, goes to sporting matches, I'm struggling to see what the scandal is."
But speaking on the same programme, Scottish Labour deputy leader Jackie Baillie said the issue was a scandal.
She added: "You need to think about what your priorities are.
"When social care is in crisis, why are you going to football games?"
And Scottish Tory finance spokesman Craig Hoy said his party had made "the very reasonable ask" of the Scottish government for minutes of the meetings held at the matches to be published.