The Board of Community Health Councils (CHCs) is refusing to say why chief executive Tony Rucinski was suspended.
Emails show that before his suspension Dr Rucinski raised concerns the board's chair Mutale Merrill may have been influenced by a government minister to stop him doing media interviews.
Ms Merill said she does not accept the emails' content is "factually correct".
Dr Rucinski said he has been "instructed not to comment."
The organisation describes itself as the "independent voice of patients" in Wales.
It and the seven CHCs it oversees had an annual budget in 2015-16 of Â£3.8m.
Dr Rucinski was appointed as chief executive of the Board of Community Health Councils in a newly-created role in July 2015.
At the time, he told BBC Wales that he had been "put in place to make things happen".
He said he wanted CHCs to become a "much more proactive and effective patient voice".
Four months later the Welsh Government appointed Ms Merrill as the board's new chair.
Dr Rucinski was then suspended in February 2016.
Several sources have told BBC Wales that there was tension between Mr Rucinski and Ms Merrill prior to his suspension.
In emails written to Ms Merrill before his suspension, obtained by BBC Wales, Mr Rucinski raises concerns about being stopped from doing interviews on a Welsh Government digital health initiative in December 2015 and on a report by the OECD think tank comparing UK health services in February 2016.
In the emails Dr Rucinski stated that his job description involved doing media interviews and suggested he felt Ms Merill's instructions to him not to do interviews may have been influenced by a meeting with a Welsh Government minister.
He wrote: "I am genuinely concerned about the comments you have relayed from your meeting with the minister."
Following his suspension, a board meeting was held in which Ms Merrill appears to try to explain the disagreement over media coverage between her and the chief executive.
The minutes state that Ms Merrill said a "media embargo" had "only been imposed on the chief executive regarding this one news item [the OECD story]", and "it was noted that there was some context behind this decision which could not be shared, however the board chair had required the chief executive to provide a briefing prior to the commenting on any issue in order to decide the best approach and deliver the message to the media".
"A conversation regarding a need for a media protocol had been discussed with the chief executive," the minutes said.
The document also said that the chief executive had shared a text message from Ms Merrill with staff "without her knowledge and without context of previous discussions".
Following his suspension Dr Rucinski claimed in an email to the Wales Audit Office in April 2016 that Ms Merrill "informed me verbally that the minister had instructed her to not let me do any further media engagements or public appearances".
In that email he also said he believed "the independent voice of patients and the public in Wales has been gagged during a crucial time for healthcare debate nationally".
Alyson Thomas and Clare Jenkins are in "acting chief executive" roles.
Dr Rucinski was previously chief executive of the Macular Society from March to November 2014.
Ms Merill said: "I can confirm on behalf of the Board of Community Health Councils in Wales that there are ongoing personnel processes relating to the chief executive officer and due process is being followed in respect of those matters."
Ms Merill added that she did not accept that Mr Rucinski's allegations in the emails were factually correct and said she was unable to provide further comment at this stage whilst internal processes are ongoing.
Dr Ruckinski said: "I have been instructed not to comment."
BBC Wales understands the Welsh Government was made aware of the suspension.
A spokesman for Welsh ministers said: "The suspension of Mr Rucinski is wholly an internal matter for the CHC Board.
"It is not appropriate for us to comment any further."
A spokeswoman for public spending watchdog the Wales Audit Office said: "We have received correspondence on this matter but after careful consideration we have concluded that it seems to fall outside of the remit of the auditor general, though we will naturally keep a close eye on any developments."
The head of the patients' watchdog has been suspended on full pay since February 2016, BBC Wales understands.