The parliamentary education committee heard evidence that there could be a conflict of interest for the inspectorate if it is given an independent role during the consultation phase of a school closure, when it is asked to comment on educational aspects, and later asked to give advice to Scottish ministers during the call-in phase.
The committee's report on Stage 1 of the Schools (Consultation) (Scotland) Bill, a preliminary step before it decides whether to support the legislation or not, also urged the Government to apply "special factors" to all schools facing closure - not just rural schools.
The Government wants the impact on a local community of closing its school; pupil and staff travelling arrangements; and viable alternatives to closure to be taken into account in any decision on a proposal to close a rural school.
Karen Whitefield, Labour convener of the education committee, said: "We have heard convincing arguments that the special factors for rural school closures should be applied to all schools, and we have recommended the Scottish Government reflect on this.
"We would also like clarification on what the Government regard as `material consideration' to justify a call-in by ministers." The term appears in the context of ministers' right to call in any school closure proposal if it is believed a council has failed to follow procedures or to take a "material consideration" into account.
In its report, the committee notes the evidence from a Scottish Government official that "a failure `to take proper account of a material consideration' might cover a situation in which the council's consultation report fails to refer to or ignores a large body of opinion in the consultation responses".
It also refers to evidence from Fiona Hyslop, the Education Secretary, who said: "The problem in defining what would be included is that you would either broaden the number of referrals or specify a tick-box list of what would be called in. A material consideration is factual content that clearly and obviously should have been made available at the start of the process."