It accused the Commissioner of failing to monitor the numbers and whereabouts of displaced Kosovars, and of allowing the Macedonian government to deport them against their will, splitting families.
"Many refugees are not registered," the organisation said. "Without registration, refugees are not individuals and have no rights and families cannot be reunified ... families were and still are being separated and transported to camps and other countries, sometimes without consent.
"MSF is extremely concerned that the minimum standards for the assistance and protection of refugees have been ignored," their statement said.
Aid workers and Nato soldiers on the ground privately have been making similar complaints for days, since the exodus began to choke the borders.
They say the UNHCR is disorganised and has left the burden of caring for the refugees to the Macedonians, whose Slav-dominated government wants only to get rid of them, and to Nato, which is a military, not a humanitarian organisation.
"Nato is neither responsible nor able to co-ordinate humanitarian relief activities for refugees - nor should it be."
The UN High Commissioner for Refugees, Sadako Ogata, admitted yesterday that it will be days before order is restored in Macedonian refugee camps. She said she has no means of helping those Albanians who were forcibly returned to Kosovo by the Serbs when Belgrade closed the border.
"I cannot do anything right now because I can't go into Kosovo without security being assured," she said.
She had spent a day visiting refugee camps and talking to political leaders in the Macedonian capital, Skopje.
"I am helpless. At the same time I am extremely concerned about the situation over the border with Kosovo," she added. Between 120,000 and 130,000 refugees from Kosovo are still inside Macedonia, about half of them billeted with ethnic Albanian families in the predominantly Albanian western part of the republic.
Mrs Ogata conceded that "we have learnt many lessons", but said it would be "a matter of days" before the situation was under control.
"Criticism is being given freely by many people many times. I'd like Medicines Sans Frontieres to join us in putting this into practice," she said.
Plans to airlift refugees to foreign countries, including Britain, appear to have been suspended. "The British Government's thinking, as well as that of myself, is that it is best to host refugees in the area neighbouring their own country," Mrs Ogata said.
The tension in Macedonia took a new and potentially damaging turn yesterday when the army confirmed a 27-year-old soldier was shot dead in a fire fight with unknown ambushers shooting from inside Kosovo.
At first there was speculation it may have been Serb forces. There was also speculation that the shooting may have been carried out by members of the Kosovo Liberation Army.Reuse content