In the film, Watson said his views about intelligence and race had not changed since 2007, when he told a magazine that he was "inherently gloomy about the prospect of Africa" because 'all our social policies are based on the fact that their intelligence is the same as ours - where all the testing says not really'.
"The Laboratory condemns the misuse of science to justify prejudice", its statement added.
Watson's new comments came in an on-camera interview with Mark Mannucci, producer of a documentary that aired last week on PBS as part of its "American Masters" series, which profiles individuals who have made a major contribution to American culture.
In the 2007 article Watson went on to avow that, while he wanted everyone to be equal in terms of intelligence, "people who have to deal with black employees find this is not true".
This time the laboratory is stripping him of his remaining honorary titles, including honorary trustee and chancellor emeritus.
The board of trustees at Cold Spring Harbor Laboratory on Long Island described the views of Dr Watson as reprehensible.
In 1962, the team was awarded a Nobel Prize in Physiology "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material".
Watson, as a young post-doctoral student at Cambridge, worked with Francis Crick to unravel the DNA molecule's structure.
Cold Spring Harbour Laboratory acknowledges and appreciates Dr. Watson's substantial scientific legacy, including his role as founding director of the Human Genome Project and his critical leadership in the development of research and education at the Laboratory during his prior tenure as Director and President.
"I believe there is very broad support among the faculty for the multiple steps that CSHL is taking in response to Watson's horrific comments", CSHL biologist Justin Kinney told STAT. But in 2014, Watson auctioned off his Nobel medal for $4.1 million, after years of being shunned by the scientific community. "I would say the difference is, it's genetic".