"I am sure he was joking," the Portuguese forward told a news conference on Friday.
"He is a good friend of mine and he knows Portugal are a top team. He played a few times against us and never won. But I am sure he was joking as he has friends here (in the Portugal squad)," Ronaldo said.
Earlier on Friday, British newspapers quoted Rooney as saying "it would be nice" to see Portugal not qualify as they had knocked out England in their last two appearances in major tournaments, the 2006 World Cup and Euro 2004.
"When we didn't qualify for Euro 2008, we (the United players) got a lot of stick (from Ronaldo)," Rooney said.
England have already qualified for next year's finals in South Africa while Portugal are third in Group One and must win both their remaining matches against Hungary and Malta, while hoping Sweden drop points, to reach the playoffs.
"Knowing him, I know why he said that; it's because it shows his respect for Portuguese football and Ronaldo particularly," Queiroz told the news conference.
