A controversial bidding process for the right to host the 2018 and 2022 World Cups was beset by allegations of corruption, leading to a long period of soul-searching for president Sepp Blatter.
Former FIFA presidential candidate Mohamed Bin Hammam was handed a lifetime ban for bribery in July while Jack Warner, a FIFA vice-president and president of the confederation governing football in North and Central America and the Caribbean (CONCACAF), resigned from all football activity in June having been charged with the same offence.
The organisation were then forced to deny claims from Warner that he had been awarded World Cup television rights for as little as a dollar as a reward for supporting Blatter.
And Scudamore told talkSPORT: "FIFA have had their difficulties, it's very hard to have huge regard for the institution the way it's performed in the last couple of years.
"Whilst one has to have a working dialogue with everyone in football and whilst I take part, I think I'm a constructive critic of what they do."
Scudamore also gave short shrift to the prospect of the 2022 World Cup being switched to winter because of the oppressive summer temperatures in host nation Qatar.
"All sorts of gloves would come off, it's just a ludicrous prospect," he said. "All leagues across the world are used to this pattern."
FIFA security chief Chris Eaton this week mentioned the Premier League when warning that no league is immune to the threat of corruption.
And Scudamore responded: "We're not immune to the threat but I am very confident we don't have any instances where games have been manipulated.
"There are early-warning systems through betting patterns and there's a huge education system with the PFA and FA.
"The rewards are high and good - although that's not a guarantee, it does play a part, it's one of the very few upsides of players being paid so much.
"We can't be complacent but I don't think there's any evidence."
Scudamore also defended the league against Arsenal manager Arsene Wenger's complaints this week over the scheduling of television games.
Wenger claimed "some teams have advantages in relation to the fairness of the competition" after the scheduling of this season's Christmas fixtures.
But Scudamore said: "The contracts are clear, the broadcasters have the right to choose.
"The only rules we have are we don't make anybody play within 72 hours of another game unless we've actually planned a fixture programme, like at Christmas, with only a two-day gap."
The league supremo is confident the competition's reputation has not been damaged by the recent racism storm surrounding Liverpool forward Luis Suarez.
The Uruguay international was banned for eight games after being found guilty of racially abusing Manchester United defender Patrice Evra.
Scudamore said: "The way the game reacted was right - a hearing was held, an intelligent man listened to all the evidence and made his decision, that's what the rulebook provides for.
"Once the decision was made, I think Liverpool have done the right thing by not appealing against the decision and by trying to put it behind them.
"It's a shame that it's happened, but I don't think it's hugely damaging - I think if anything, our reputation for dealing with this matter has been enhanced."