Their absence has embarrassed the Prime Minister because David Blunkett, the Education and Employment Secretary, launched a campaign last week to persuade parents not to take holidays during term time.
Mr Blunkett is to hold talks with teaching unions and holiday companiesin response to complaints by head teachers about the number of unauthorised absences. But the initiative rebounded on the Government yesterday when two of the teaching unions criticised Mr Blair, who was also given a public rebuke by the head of the school attended by his two sons.
David Hart, general secretary of the National Association of Head Teachers, said: "It is unfortunate that the Prime Minister should be setting an example of this nature, given the policy which his own Government is trying to enforce."
Mr Hart said all parents of children at schools that had a policy of no unauthorised absences for holidays had a duty to stick to the rule. "If you allow one family to get away with it, then what are the other families going to think?
"If the Blairs had wanted to cut into the term time, then it was open to them to obtain the head's permission and get an authorised absence. The head, for all I know, might have given permission," he said.
Nigel de Gruchy, general secretary of the NASUWT teachers' union, said: "This is a good example of why politicians should keep their mouths shut and not try to lecture other parents. They try to tell teachers how to run schools and end up being embarrassed themselves."
John McIntosh, headmaster at Oratory School, west London, criticised what he called the "unauthorised absence" of Mr Blair's sons and said he usually wrote a stern letter to parents who allowed their children to stay away during term time.
He added: "I am really tough about this sort of thing. I say to parents they must observe what I call the three Hs - haircuts, holidays and homework."
David Willetts, the Conservative education spokesman, said Mr Blair's decision had "cut the ground" from under Mr Blunkett's feet. "This is another piece of Labour hypocrisy in education," he said.
But Downing Street dismissed the controversy, insisting that Euan, 14 and Nicky, 13, would miss only one day's school. The Oratory does not return until tomorrow and they should be at their desks on Wednesday.
Kathryn, Mr Blair's 10-year-old daughter, is expected to miss two days at the Joan of Arc primary school in Highbury, whose pupils return today.
Downing Street denied the charge of double standards. A spokesman said: "David Blunkett was talking about families taking their entire holidays outside the school term and that children should not miss two or three weeks of school. That is different to missing one or two days."
The spokesman added that the Blair children were not absent without permission: "Mrs Blair wrote some time ago to the headmaster explaining that the children would miss a day."Reuse content