"Despite the malicious fallacies, the couple is looking forward to a long and happy life together as a family," a statement issued by their publicist said.
Tom Cruise, 43, and Katie Holmes, 27, are expected to get married later on this year.
"Mr Cruise and Ms Holmes are still engaged and are moving forward with their wedding plans, as well as planning for the arrival of their child," the statement went on.
The couple had begun seeing each other last April, and became engaged just two months later when Tom Cruise proposed to the former Dawson's Creek star at the Eiffel Tower in Paris.
They are currently living at Cruise's Beverly Hills home in Los Angeles.
Life & Style magazine defended its story saying it was based on information from unnamed sources who have been described only as "multiple insiders".
"We stand 100% behind our story," claimed a spokesperson for the magazine.
Tom Cruise, who besides his success as an actor is known for his outspoken support of the Scientology cult, has been married twice before, and has two adopted children with his previous wife, the actress Nicole Kidman.
Cruise makes a return to the big screen in Mission: Impossible III, due to be released in early May.
Hollywood movie star Tom Cruise has said a story that suggests he is going to split from his pregnant fiancee Katie Holmes is "100% false".
