The SNP has been accused of adopting a cult of slavishness to the party's leadership rather than trying to hold the government to account.
Opposition parties vented their anger on Tuesday after complaining that the SNP blocked a Public Audit Committee report which criticised controversial police reform.
Labour committee member Ken Macintosh brought the row to Holyrood's main chamber following First Minister's Questions today amid loud jeers from the SNP benches.
One SNP convener was called to the Presiding Officer's office for his persistent shouting during Mr Macintosh's request for guidance on how to address "sheer government obsequiousness" in committees.
Ms Marwick confirmed that the matter may be referred to the Standards, Procedures and Public Appointments Committee, which scrutinises MSPs' conduct, and also to the forum of Holyrood conveners which she chairs.
Mr Macintosh said committees have been "a place for rigorous debate" for over a decade.
"Never until the current session have they been a place for sheer government obsequiousness," he said.
"All members are expected to show loyalty to their own political party, but each of us has a parliamentary duty and a responsibility to the public to hold the government to account.
"In deliberately trying to downplay, obscure or simply whitewash evidence to any of our parliamentary committees, members are in danger of putting the interests of the government or their own party first.
"That does no-one any favours. There is an expectation that all parliamentary committees, perhaps most of all the Public Audit Committee, will be robust but fair and objective in its deliberations.
"I would appreciate your guidance on how we ensure that the hard-won trust won over several successive parliaments is not lost.
"Could you advise if this is a matter for investigation by the Standards, Procedures and Public Appointments Committee."
Ms Marwick said: "Conduct in the committees and how each committee approaches any given issue is a matter for those committees and for conveners.
"Where any member considers that there is a failing in parliamentary procedures it is open to that member to write to the Standards, Procedures and Public Appointments Committee to request an investigation.
"Members may also write to the conveners' group to ask that body to consider the issue."
SNP Education and Culture Committee convener Stewart Maxwell was called to Ms Marwick's office for persistently shouting out during Mr Macintosh's point of order.