Amid signs of Tory misgivings about support for the Government over the attacks, the Labour MP Diane Abbott clearly irritated Mr Cook by claiming that the attacks were on a "slender" justification of preventing a humanitarian catastrophe.
The left-winger defended Sir John Stanley, a Tory member of the committee and former defence minister, after he was involved in angry exchanges with Mr Cook for questioning the conduct of the Nato offensive.
In some of the sharpest clashes with MPs since the conflict began, Mr Cook turned on Sir John for claiming Nato had been warned that President Slobodan Milosevic would respond to the attacks by increasing ethnic cleansing in Kosovo and had failed to realise the consequences of its actions.
Mr Cook said he would "vigorously rebut" the suggestion that the Nato bombing had caused the "ethnic cleansing" of Albanians from Kosovo.
"I personally deprecate those who play Milosevic's game of suggesting it is Nato that is to blame for the ethnic cleansing because it comes close to accepting he is justified in responding to the Nato bombing by the barbarity with which he has behaved.
"Nobody was saying in 1940 we should stop bombing Hitler because he is killing the Jews. Nobody was making that linkage. It was because of his politics and his fascism that he was carrying out the genocide. It is exactly the same with Milosevic and the Kosovars," said Mr Cook.
Ms Abbott protested to the Foreign Secretary: "It is not a substitute for a reasoned defence to accuse people of being an apologist for Milosevic. That is not a serious defence for what you have been doing."
Later, John Prescott, the Deputy Prime Minister, heard further Tory misgivings over the "shifting and the confused military and political objectives" of the Nato action.
Peter Lilley, deputy Tory leader, warned British troops could be "overstretched" because of the cuts outlined in the Strategic Defence Review.
Peter Luff, Tory MP for Mid Worcestershire, asked: "Why yesterday did the Prime Minister say to the House that Serbian brutality in Kosovo was planned well in advance, when three weeks ago Robin Cook and Clare Short [Secretary of State for International Development] were both saying that no one could have anticipated the Serbian reaction to the bombing campaign and, incredibly, that to put humanitarian assistance in place in advance would have made us complicit in Milosevic's campaign?"
But Mr Prescott, standing in during question time for Tony Blair who was at the European Union summit in Brussels, said no one could have envisaged the horrific actions seen Kosovo: "I don't think there's any doubt the general public will certainly ... accept that these events were going on. The scale of them no one envisaged."
His claims were supported by Clive Soley, chairman of the Parliamentary Labour Party, who warned Tories not to end the bi-partisan consensus on Kosovo.Reuse content