Sources yesterday claimed Nationalist backbenchers were attempting to suppress a public petition calling for independence referendums for Orkney, Shetland and the Western Isles.
In a separate case, the SNP-dominated finance committee was accused of withdrawing an expert's invitation to give evidence after he submitted a report that contradicted government claims about an independent Scotland's membership of the EU.
Labour MSP Michael McMahon claimed SNP MSPs were acting as "shields" for ministers, and warned increasing control over committee business was "not healthy for the democratic process in this country".
The latest claims emerged after opposition MSPs on Holyrood's public audit committee hit out after producing a minority report on the troubled launch of Police Scotland. The SNP majority on the watchdog committee voted through an official report that removed criticism of Kenny MacAskill's handling of the police force mergers last year.
Labour's Hugh Henry, the committee convener, said it was a product of a "cult of obedience and slavishness" imposed on SNP backbenchers.
One of the new claims relates to a petition lodged with the public petitions committee two weeks ago calling for constitutional referendums for Orkney, Shetland and the Western Isles.
A group of campaigners want islanders to have a choice of becoming independent, remaining part of Scotland or, in the event of a Yes vote in September's referendum, staying in the UK.
Sources close to the committee said SNP MSPs were attempting to keep the petition off the agenda - even though MSPs are obliged to consider a properly lodged petition - to prevent discussion of an issue that would potentially be embarrassing for Alex Salmond.
SNP members of the finance committee were also accused of protecting ministers after an expert witness, academic Matt Qvortrup, failed to appear before MSPs yesterday as planned. He had submitted written evidence stating there was "no guarantee" an independent Scotland would be admitted to the EU or UN.
His submission was not published because his invitation to appear in person was withdrawn. However, it was released following a request by Labour finance spokesman Iain Gray.
The Labour MSP said: "The SNP choose to play games, first insisting on witnesses they expect to be helpful to them, and then dumping them when their views don't suit the SNP line. The decision to withdraw Matt Qvortrup from giving evidence based on his written submission makes clear that the SNP will actively seek to suppress views if the conclusions don't match their expectations."
Mr McMahon said: "Too often backbenchers see themselves as shields for ministers. It is not healthy for this parliament and for the democratic process in this country."
An SNP spokesman said: "We reject and deplore these partisan attacks, which are not supported by the facts. SNP MSPs on committees take their roles very seriously.
"It must be recognised that the cross-party nature of committee work means that there are sometimes areas on which members cannot reach agreement. In these cases, votes are taken and a democratic decision is reached. These allegations are more evidence of the opposition parties attempting to undermine the Scottish Parliament's committee system."