In 2007, he said he was "inherently gloomy" about Africa's prospects because Western policies towards the continent assumed Africans were as intelligent as Europeans. "The laboratory condemns the misuse of science to justify prejudice".
Watson, who discovered the double-helix structure of DNA with partner Francis Crick in the 1950s, said in "American Masters: Decoding Genetics" earlier this month that genes are responsible for inferior intelligence among blacks.
But Cold Spring Harbor said it was now stripping him of those titles after he said his views had not changed in the documentary American Masters: Decoding Watson, aired on USA public broadcaster PBS earlier this month. In that interview, he also said he wished racial equality was real but "people who have to deal with black employees find this not true".
In a statement, CSHL said in light of Dr Watson's views the laboratory had taken "additional steps" against Dr Watson, including revoking his honorary titles of chancellor emeritus, Oliver R. Grace professor emeritus, and honorary trustee.
The lab ejected Watson from his role as chancellor and from administrative duties in 2007 following previous racist remarks - even though he retracted and apologized for the statements.
He claimed the differences in intelligence between black and white people was borne out by their average scores in IQ tests.
The 2019 PBS film reveals that Watson's views on intelligence and race have not changed.
James Watson the Nobel Prize for the 1953 discovery of the DNA's double helix structure.
Mr Watson has not yet issued a comment on the development.
"The statements he made in the documentary are completely and utterly incompatible with our mission, values, and policies, and require the severing of any remaining vestiges of his involvement", Simons and Stillman said. But in 2014, Watson auctioned off his Nobel medal for $4.1 million, after years of being shunned by the scientific community.
Watson had always been associated with the lab, becoming its director in 1968, its president in 1994 and its chancellor 10 years later.