Ministers were told to treat Holyrood with respect by its presiding officer after announcing a proposed streamlined system of regulating industries in an independent Scotland.
Tricia Marwick said she expected any major policy announcements by the Scottish Government to “always be made to the Parliament” in the first instance.
It came after Liberal Democrat MSP Tavish Scott accused the Government of treating Parliament with “contempt” by making the announcement without consulting other members.
He said: “It may be inconvenient for ministers to have to stop what they are doing and report to parliament, but that is the democratic system.
“We now have a situation where the Scottish Government treats this Parliament with contempt.”
Ms Marwick replied: “Can I ask that the Scottish Government reflect carefully on whether the method used for these particular announcements has been appropriate, and follows the good practice guidance on making announcements in the Parliament.
“Can I add that the Scottish Government should always ensure that it treats this Parliament with the respect it deserves.”
Following Ms Marwick’s statement, a Scottish Government spokesman said Parliament had been notified and the document was sent to four different committees on Wednesday night.
The Scottish Government paper, launched by John Swinney during a meeting with business leaders in Stirling, says one or two bodies could be set up to oversee energy and telecommunications, postal services, water and rail.
Ministers say such a set-up could benefit both businesses and consumers, as well as save money for the public purse.
Mr Swinney said an independent Scotland could make sure the “right systems” were in place, while the paper highlights lower water bills north of the border, with people paying on average £50 a year less for water and sewerage services in 2012-13 than in England and Wales.