The first minister has distanced himself from comments by Communities Minister Malcolm Chisholm over the treatment of failed asylum seekers.
Dawn raids on asylum seekers have sparked a series of protests
Mr Chisholm made it clear that the Scottish Executive wanted an end to the controversial policy of dawn raids prior to deportation.
However, a source close to Jack McConnell disowned those comments.
As the immigration minister visited Scotland, Mr McConnell denied he had been over-ruled by the Home Office.
Ministers faced loud protests following the deportation of the Vucaj family in September.
Witnesses said the family, who had been living in Drumchapel area, endured tough tactics during the eviction and there were reports of friction between the Home Office and Scottish ministers.
Responding to protests about dawn raids in September, Mr Chisholm told the BBC: "We know there's great concern in Scottish society about what's happened and we share those concerns.
"They're totally unnecessary, heavy handed and over the top."
But the first minister's official spokesman said Mr McConnell "...has never raised the issue of ... whether dawn raids should cease or continue".
Nicola Sturgeon, leader of the Scottish National Party group at Holyrood, went on the attack at First Minister's Questions.
"Was Malcolm Chisholm speaking on behalf of the executive?" she asked.
Mr McConnell chose not to answer Ms Sturgeon directly.
Her criticism was echoed by the Scottish Socialist Party and at least one Liberal Democrat.
Green MSP Patrick Harvie told Mr McConnell: "We want clarity about how the executive will live up to its acknowledged responsibilities.
"That is not too much to ask, and this is not too soon to ask it.
"Child welfare is his responsibility and it seems that he is being blocked by the Home Office. "
But the first minister denied he had been snubbed by the Home Office.
On the contrary, Mr McConnell argued, he had carried out the will of Holyrood and expressed concerns about the heavy handedness of the dawn raids.
He insisted the pressure was causing Westminster to review its procedures for the whole of the UK.
The Vucaj family were deported after a dawn raid
Mr McConnell added: "This issue is not about the personal egos of politicians, or their relationships with other politicians - or anything else.
"It's about the children. The children and the impact on them."
Earlier, the UK immigration minister defended dawn raids to remove failed asylum seekers, describing them as "central to a robust" policy.
Tony McNulty said there would be no special protocol with the Scottish Executive to change the way removals involving children were handled.
He added that any changes to the way dawn raids were carried out would have to be introduced right across the UK.