The Queen is to be legally obliged to abide by new nature conservation measures at her Balmoral estate.
Mr Canavan said Balmoral should come under the legislation
It follows a promised Scottish Executive u-turn under pressure from Falkirk West MSP Dennis Canavan.
He argued that Holyrood could not pass one law for the Queen and a different one for other landowners.
The Nature Conservation (Scotland) Bill is aimed at protecting the environment, conserving biodiversity and safeguarding natural habitats.
The proposed legislation would apply to the Crown estates, but not the Queen's personal property such as Balmoral.
Mr Canavan argued in committee that this was not right.
The executive had argued that Balmoral had a good nature conservation record and insisted the Palace had not asked for any special treatment.
But ministers have promised to overturn the extension at the bill's next stage through parliament.
Mr Canavan had a similar success in 2003 when he managed to amend the executive's Land Reform (Scotland) Bill to allow ramblers to gain some access to Balmoral.
He said: "Balmoral Estate contains some of the most outstanding natural environment in Scotland.
"The Scottish Parliament has a duty to conserve it instead of just leaving it to the discretion of the Queen or her factor."
Deputy Environment Minister Allan Wilson called on the environment and rural development committee, which is carrying out line-by-line scrutiny of the bill, not to support Mr Canavan's amendment.
He urged him to withdraw for now, promising the executive would bring forward its own amendment at a later stage to satisfy his demands.
Mr Canavan refused and the committee voted 6-3 against him.