The actress, who plays Lady Cora Grantham, said that the ITV period drama wasn't "set up" to tackle the gravity of WWI.
"There is a slightly different tone to the second season," she explained to LA Times. "It's kind of a taste thing. And the show in the first season was more to my taste than the show in the second season.
"[We had to] deal with this huge elephant. In some ways, Downton Abbey wasn't set up for that."
However, McGovern has since denied that her remarks were a criticism of the second run, clarifying: "I am horrified that my comments about the second series of Downton Abbey have been taken out of context and misinterpreted. I was in no way criticising the second season or implying that I loved or enjoyed it any less.
"When asked about the second series I said that the tone differed slightly from the first. There would be some people who would naturally prefer the more domestic detail of series one and others who would love the faster pace and heightened drama of the war years.
"That does not translate that series two was any less entertaining than series one - and many millions of people around the world agree with me.
"Julian Fellowes is a brilliant writer and I am proud and privileged to be part of this show. The third season is so rich with character detail, storylines and new faces that I can't wait for people to see it."
It has been announced that Shirley MacLaine will portray Lady Grantham's mother in the upcoming third series.
Ed Speleers, War Horse's Matt Milne, Cara Theobald and Lucille Sharp have also joined the Downton Abbey cast.
> 'Downton Abbey': Major character to die in series three