An Omani court last month sentenced six men to 20 years while 24 were jailed for periods of seven to 10 years. One received a one-year sentence.
The state news agency ONA said on Thursday that Qaboos issued a decree granting them a pardon but gave no more details.
The group includes preachers, Islamic scholars, university professors and government figures.
The government had accused the men of trying to set up Islamic clerical rule in Oman.
There was no suggestion they had links to radical Sunni group al-Qaida led by Usama bin Laden.
Witnesses at the trial said the group denied planning to overthrow the government and insisted that their aim was to strengthen the Ibadi Muslim sect to which Qaboos and the majority of Omanis belong.
The imamate, a centuries-old Ibadi tradition of politico-religious leadership by an imam, was abolished in Oman in 1959.
The men were arrested in December as part of an unprecedented crackdown on Islamists in Oman.