A debate on the treatment of failed asylum seeker families has prompted a pledge from ministers to lobby the Home Office to consult Scottish authorities.
The Vucaj family made a last-minute plea to remain in Scotland
Campaigners have raised concerns over how immigration officers remove children for deportation in dawn raids.
The Green Party debate brought damning criticism of the level of force used.
Green co-convener Robin Harper said the Scottish Executive must "pull out all the stops" to protect the "vulnerable" children of asylum seekers.
Robert Brown, Deputy Minister for Education and Young People, said decisions over whether people should be granted asylum or should be deported remained reserved to Westminster.
But he added: "This doesn't mean that the executive is gagged on matters of asylum and immigration, particularly where they affect children."
First Minister Jack McConnell raised the issue at Wednesday's cabinet ahead of the Holyrood debate and one of his ministers discussed it with a Home Office minister shortly after that meeting.
The executive has requested a "protocol" with the Home Office to ensure greater involvement of devolved agencies such as education authorities and police before action is taken to remove children pending deportation.
Mr Brown told parliament that Scottish ministers had an "open and uninhibited" dialogue with their Home Office counterparts.
He added: "I can't comment on individual cases but I want to make sure and I'm determined that in every case involving children we make sure the Home Office works closely with services for children and young people prior to the removal of the family.
"And we will in fact convey our concerns from the debate today to the responsible ministers in London."
The debate followed the public outcry over the dawn raid on the home of the Vucaj family in Glasgow, where up to 16 immigration officers were reported to have been involved and one person under the age of 18 was alleged to have been handcuffed.
The Kosovans' treatment provoked anger among pupils at Drumchapel High School, which the Vucaj children attended, as well as an unprecedented attack from Children's Commissioner Kathleen Marshall.
Opening the debate, Mr Harper branded the UK's asylum and immigration system "a disgrace", attacking its "draconian measures" which he said criminalised innocent people.
He added: "From public bodies to children's organisations to school friends, there is recognition that these scandalous immigration practices are causing trauma and distress, and blatantly disregard children's rights.
The Vucajs were taken to Yarlswood Removal Centre in Bedfordshire
"When Scottish society expresses such profound concern it is right to expect the Scottish Parliament to do likewise."
As pupils from Drumchapel High looked on, Glasgow Socialist MSP Tommy Sheridan suggested that their intervention and compassion had "shamed" Scotland's political leaders, an accusation echoed by Scottish National Party (SNP) leader Nicola Sturgeon.
And SNP MSP Christine Grahame heavily criticised the executive move as a last-minute "Jack-fix-it".
She said: "It has been debated over and over again in this chamber and to expect the parliament to welcome this - come on."
She told Mr Brown: "London pays no attention to the jurisdiction of the reporter to the Children's Panel, pays no attention to what the commissioner for children has to say and will pay no attention to this wishy-washy amendment that you've put down today."
Conservative MSP Mary Scanlon said the executive's position addressed the problems faced by asylum seekers and their families in Scotland, but called for enhanced child protection training and criminal records checks in immigration centres such as Dungavel.
"We support the condemnation of the so-called dawn raids, the handcuffing of children and the removal of children by large groups of officers in uniform and body armour," Ms Scanlon told MSPs.
Setting out his party's position, Liberal Democrat backbencher Jeremy Purvis said too many people were detained unnecessarily in removal centres for too long.
"There are many alternatives to detention, for example tagging or voice recognition techniques, or indeed the requirement to report daily to a police station," he said.
Parliament backed the Scottish Green Party motion, but only after it had been altered through an executive amendment.
The amendment retained much of the original motion but removed a section stating that such practices were "unnecessary and cause fear and distress to the children concerned".