- This article was clarified on 20 December 2018; see final paragraph
Helen Stephenson, chief executive of the commission, wrote to all 118 charitable think tanks last week telling them to "retain balance and neutrality in their research work".
But in an email to its charity clients this week, Bates Wells Braithwaite said the advice had caused concern.
The email said the tone of the advice appeared to be at odds with recent government statements about the contribution charities should make to public debates.
It highlighted as examples Prime Minister Theresa May's pledge that contracts and grant agreements should not prevent charities from speaking out against government policy, and a quote by Mims Davies, the Minister for Sport and Civil Society, saying "independence and freedom of speech are absolutely vital in this sector".
The email said the advice placed "undue emphasis" on ensuring a think tank's outputs, such as reports and seminars, were balanced and neutral.
"We consider this to be an unrealistic and undesirable requirement of charitable education," it said. "Educational research will inevitably reach conclusions and the research would often be of limited value if that was not the case."
BWB also questioned the part of the advice saying that researchers should not be "linked to a particular view or opinion" because it ignored the "practical reality that many academics and researchers will be linked to particular schools of thought".
It added: "The key issue is that any assumptions underlying a research product should be clearly explained and the conclusions derived from a clear, educational process of analysis, allowing the reader to make up their own mind on whether they agree with the assumptions and resulting conclusions."
It also questioned whether it was right for the advice to say it was unacceptable for audiences at think tank events to be addressed only by people with the same views.
"This seems to ignore both the practical reality that educational lectures are regularly given by a single academic or expert, such as in charitable universities and other seats of learning, and also that it will often be unreasonable to view a single event in isolation, rather than within a broader programme of output," the email said.
Simon Steeden, a partner at BWB, told Third Sector: "The guidance needs a rethink with input from the wider community of charitable think tanks to avoid unreasonable and unintended consequences.
"We hope the commission will be open to that. It recently took a very positive approach to consultation over equally sensitive new guidance for charities connected with non-charitable organisations, which is likely to be much improved as a result."
A commission spokeswoman said: "Our recent regulatory alert was a reminder to trustees of their existing legal obligations and duties.
"We have received some comments back and will be looking to engage with some of those charities that have responded to discuss and provide further clarity in the New Year."
- Some references in the article to guidance have been amended at the request of the Charity Commission to make it clear that its regulatory alert did not constitute official guidance