The Foreign Secretary said in a Commons statement it was "crucial" the undertaking of the Russian Foreign Minister, Igor Ivanov, that there would be no more "surprise moves" was "fully respected".
Despite his criticism, Mr Cook urged MPs to keep a "sense of perspective" on the number of Russian troops involved, saying: "There are still only 200 Russian troops in Kosovo, compared with 14,000 Nato troops.
"Nevertheless, it was plainly unsatisfactory that Russian troops should have entered without co-ordination with the other forces in Kosovo," he said. "Yesterday I spoke at length with Mr Ivanov and we agreed there should be no more surprise moves.
"He gave an undertaking that Russia would not deploy any further troops without prior agreement with Nato.
"Earlier undertakings about Russian deployments have not all been respected. It is crucial that this undertaking should be fully respected."
Mr Cook stressed that there was no prospect of any move towards the partition of Kosovo.
"The unilateralism is disturbing and that is not to be repeated if we are going to achieve the confidence and trust and agreement we need of a centrally co-ordinated operation.
"We want the Russians to be there. We want a bigger Russian contribution to secure the peace in Kosovo, but it has to be co-ordinated."
Michael Howard, Conservative foreign affairs spokesman, said recent developments showed the extent of the problem still to be overcome and the difficult decisions that would need to be taken.
"The ultimate test of success is whether all the refugees are able to return home... There is obvious concern over the deployment of Russian forces at Pristina airport. Would you confirm that the original plans were for British paratroopers to enter Kosovo on Friday morning?"
Replying, Mr Cook said there was no "security gap" in the timing of the entry of Nato troops into Kosovo.
On the question of reconstruction, Mr Cook said: "Nobody should under- estimate the challenge ahead of us. There is a long way to go yet. We must get up every morning awake to every trick played by [Yugoslav President Slobodan] Milosevic."
Donald Anderson, Labour chairman of the Foreign Affairs Select Committee, said the suggestion the Russian deployment was a misunderstanding was a matter for "incredulity".
Ann Clwyd, Labour MP for Cynon Valley, called for economic assistance to be extended to Serbia even while Mr Milosevic was still in power.
"I want to see Serbia and Milosevic brought before a war crimes tribunal," she said.
"But I do believe that Serbia will join the international community of nations faster if we also show a willing hand to assist them in reconstructing and rebuilding their own lives."Reuse content