"I deeply regret the comments," Charles Black, one of McCain’s most senior political advisers and his chief strategist, said in a statement. "They were inappropriate."
In an interview with Fortune magazine, Black said another terrorist attack like that of 9/11 before the November presidential vote would be an "advantage" for McCain.
"Certainly it would be a big advantage to him," Black told the magazine.
A longtime influential figure in the Republican circles, Black has counseled and lobbied for every Republican candidate since 1972.
Black has emerged as McCain’s leading political adviser, right-hand man and the most visible public face of the republican campaign on television.
McCain was quick to distance himself from the controversial remarks.
"I cannot imagine why he would say it," McCain said while campaigning in California.
"It’s not true. I’ve worked tirelessly since 9/11 to prevent another attack on the United States of America. My record is very clear. If he said that, and I do not know the context, I strenuously disagree."