A statement from the family released on China Aid claimed authorities had tried to force the family to sign an agreement which would allow Peng Ming's organs to be harvested for scientific research, but they had refused.
The Communist Party has taken a hard line on Christianity since Chairman Mao came to power in 1949.
Mao threw more than 10,000 missionaries out of China at the start of his reign.
The party seized church property and killed or imprisoned Chinese Christians.
Now, Christians have the right to worship at join state-controlled churches.
Many choose to worship in house churches instead. Christians still face prejudice and even imprisonment for their beliefs.
Peng Ming's brother was later informed they had gone ahead and taken out his heart, brain and other organs.
Peng Ming's family, who live overseas, were denied access into the country for his funeral because the authorities did not want "foreign interference in China's internal affairs".
Peng Ming had been incarcerated since 2005 in Hubei Province and was serving a life sentence for publically advocating democratic reform. He died on 29 November.
The circumstances of Ming's passing remain unclear, with the death certificate giving no details of the cause.
Pastor Bob Fu, president of China Aid, expressed his condemnation of the authorities "deliberate manipulation" of Peng Ming's family members.
Christian Solidarity Worldwide's Chief Executive Mervyn Thomas said: "The lack of transparent information about the causes of Peng Ming's death is deeply troubling.
"The family's three requests - for viewing rights of his body for family members, for an independent autopsy, and for all Peng's personal possessions to be returned to his family - have not been met, and the dissection of his body, without the family's consent, can only have made their suffering more acute.
"We call on the Chinese authorities to investigate immediately and impartially the causes of Peng Ming's death and potential human rights abuses committed by the prison authorities."