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Nguyen Van Ly, jailed for eight years in 2007, is in deteriorating health, his sister told AFP shortly before government officials announced the amnesty to mark Vietnam's September 2 National Day.
Ly was convicted at a half-day trial in the city of Hue for spreading propaganda against the communist state, in a case that drew condemnation from diplomats, Vietnam watchers and human rights groups.
Prosecutors said Ly was a founding member of the banned "Bloc 8406" pro-democracy coalition, named after the April 8, 2006 date on which it was launched, and that he was also a driving force behind the outlawed Vietnam Progression Party (VPP).
"Nguyen Van Ly this time is not granted amnesty because... amnesty is only granted to persons who make progress in their rehabilitation," Le The Tiem, Vice Minister of Public Security, told a news conference.
Tiem said Ly had received amnesty once "but then he committed new violations."
Ly, who is in his early 60s, has been jailed three times since the 1970s for a total of 14 years.
In early July a bipartisan group of 37 United States senators sent a letter to Vietnam's President Nguyen Minh Triet calling for Ly's "immediate and unconditional release," saying his trial appeared "seriously flawed."
Triet signed the decision granting amnesty to 5,459 prisoners.
"The state of my brother's health has deteriorated since mid-July," after a fall in his cell in May, said Ly's sister, Nguyen Thi Hieu, who visited him last Wednesday.
"His arm and his right foot are lightly paralysed. He was walking with difficulty and needs people at his side to help him move around the room," she said, adding prison officials had given him medication.
Tiem said Ly's health "is now good."
He said that 13 people who broke national security laws were granted amnesty.
These included 11 ethnic minorities from the Central Highlands. They were convicted between 2003 and 2006 for sabotaging the policy of "national unity" or for disturbing security, a separate government statement said.
Two others, convicted in 2004 of opposition to the regime, were also freed, it said.
The amnesty comes as Vietnam says it is preparing to try another national security case involving human rights lawyer Le Cong Dinh and others recently arrested and accused of anti-state activities.
US ambassador Michael Michalak last week expressed concern over those arrests as well as Vietnam's efforts to crack down on the media and to "criminalise free speech."
Among those granted amnesty were 794 women and 19 foreigners: four Chinese, two South Koreans, four Cambodians, two Canadians, an American, one Australian, two from Taiwan and one each from Laos, Myanmar and Congo, Tiem said.