Mukoko, a former newscaster who headed the Zimbabwe Peace Project, was taken away at gunpoint in Harare on December 3 by unidentified men.
If found guilty of the charges, the activists could face the death penalty, lawyers have said.
Zimbabwe police officials have denied holding Mukoko, who had not been seen since being taken from her home on the same day as nationwide protests against the country's deepening economic and health crises.
The case has added to doubts over the implementation of a power-sharing agreement between Mugabe and opposition leader Morgan Tsvangirai, seen as a chance of rescuing the once relatively prosperous country from economic collapse.
Reports of violence
Mukoko's independent organisation monitored human rights and had compiled reports of violence at elections this year that were widely condemned outside Zimbabwe.
The state-run Herald newspaper said the activists have been accused of recruiting or attempting to recruit people for military training to topple the government.
|Mugabe has rejected growing international calls for him to step down from power [EPA]
Citing a police statement, it said some of the activists had recruited people for training in Botswana, including a police constable.
It said the plan was to "forcibly depose" Mugabe's government and replace it with one headed by Tsvangirai.
The opposition says abductions of activists have continued since a June presidential run-off in which Mugabe was re-elected unopposed after Tsvangirai withdrew from the election, complaining of attacks on his supporters.
Tsvangirai has threatened to suspend negotiations on a September 15 power-sharing agreement if arrests do not stop. He won a first round election in March, but without an absolute majority.
Talks on sharing power have been deadlocked over control of key ministries, pushing Zimbabwe deeper into crisis.
The court appearance of the rights activists came a day after Mugabe told George Bush, the US president, to stay out of his country's political affairs, calling him a "dying horse".
The White House had earlier said that it could no longer support a government that includes Mugabe.
Despite mounting criticism of his rule, there is little that Western powers can do to force Mugabe out.
Sanctions have failed to weaken him and analysts say that military intervention in unlikely because Zimbabwe is not seen as a strategic country with key resources such as oil.