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."
One area in which the league are bound by FIFA's rules is with regard to football's international transfer windows, and Scudamore again found himself in disagreement with the world governing body over this month's market.
"I think most people would say we don't particularly need one in January, (clubs) all say they don't do particularly good business," he said.
"I would also like to see it shortened in the summer. I know it would make it difficult for the promoted clubs but the fact we start our season on the 15th or 16th (of August) and we're still signing players until the end of the month is difficult."
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."