Professors Drew Scott and Andrew Hughes of the University of Edinburgh have written a letter to Alex Fergusson, the Presiding Officer of Scottish Parliament, claiming that they were ambushed and interrogated by MSPs.
The letter makes allegations that they were ambushed by Scotland Bill Committee convener Wendy Alexander and Conservative Committee member David McLetchie.
The discussion over the Scotland Bill focused on the economic impact of Scottish independence. Professor Scott claimed that independence would result in a 1.7 per cent rise in Scotland's Gross Domestic Product (GDP). Ms Alexander and Mr McLetchie questioned the validity of Professor Scott's findings to such an extent that he claimed to have been "very upset" after the hearing.
Scott and Hughes are now seeking an explanation for the incident.
In a letter to The Herald, the academics stated: "We have written to the presiding officer seeking an explanation for the extraordinary events surrounding our appearance at the Scotland Bill Committee, events which undoubtedly damaged our professional reputations.
"More importantly, we consider that these events not only undermine both the reputation of the Scottish Parliament and the willingness of others to appear before its committees to offer expert advice, they have prevented committee members from discussing with us our concerns about the adverse consequences the implementation of this bill could have for Scotland."
Green Party MSP Patrick Harvie, the convenor of the Transport Committee, claimed that Holyrood's committee system had become "polarised and partisan".
Mr Harvie said: "Parliament's committees were designed to be places where the public, civic Scotland and the professionals alike could come to share their knowledge and expertise with MSPs.
"Although they still do good work, too often they have become polarised and partisan... where those giving evidence are not given the respect and space they deserve."