The Cold Spring Harbor Laboratory said it
was acting in response to remarks he made in a television documentary which aired earlier this month.
The 90-year-old geneticist - one of three who discovered the DNA double helix - had lost his job at the New York laboratory in 2007 for expressing racist views.
But in the new PBS film, American Masters: Decoding Watson, he said his views on intelligence and race had not changed since.
He had told a magazine in 2007 he was "inherently gloomy about the prospect of Africa" as "all our social policies are based on the fact that their intelligence is the same as ours - where all the testing says not really".
Image:The 90-year-old geneticist lost his job at the New York laboratory in 2007While Dr Watson also said he hoped everyone was equal, he added: "People who have to deal with black employees find this is not true."
In the latest documentary, the molecular biologist says that genes cause a difference on average between black people and white people in IQ tests.
The laboratory branded the latest remarks "reprehensible", "reckless" and "unsupported by science", saying they effectively reversed Dr Watson's written apology and retraction in 2007.
The research centre subsequently revoked three titles - chancellor emeritus, Oliver R Grace Professor Emeritus, and honorary trustee.
The zoologist has a long-standing association with the Cold Spring Harbor Laboratory, with him becoming director in 1968, its president in 1994 and its chancellor a decade later. The lab also has a school named after him.
Dr Watson's son, Rufus, has since said his father was in a nursing home after a car crash in October. He said the scientist's awareness of his surroundings were "very minimal" and rejected the notion he was a "bigot".
He said: "My dad's statements might make him out to be a bigot and discriminatory... [but] they just represent his rather narrow interpretation of genetic destiny
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