Castro, 83, has not appeared in public since July 2006 when he underwent emergency intestinal surgery and provisionally ceded power to Raul Castro.
"He is thin but he looks good, and according to our director, he is very good mentally," a comment accompanying the photos on the blog of Rosa C. Baez said.
Baez wrote that Castro was spotted making a "surprise visit" to the think-tank and stopped to greet and "throw kisses" to the group that waited for a chance to see him.
The photos were also posted on the blog of Norelys Morales, a well-known Cuban television journalist.
Morales told The Associated Press news agency she got them in an email sent to various people by a worker at the think-tank, but she would not reveal the worker's name.
The visit to the scientific centre celebrated the 45th anniversary of its creation in July 1965, the story on the cubadebate website said.
Last year, Hugo Chavez, the Venezuela's president and a close ally of Castro, said the frail leader had been going for walks near his Havana residence, but this was never confirmed by the government and no photographs were made public.
Castro ruled Cuba for 49 years after leading the 1959 revolution that toppled Fulgencio Batista, a US-backed dictator.
He dominated Cuban life, often making long, televised speeches and numerous public appearances.
He resigned the presidency in February 2008 and Raul Castro, 79, officially took over as president in a vote by the National Assembly.