Special Envoy Alvaro de Soto called the decision unhelpful and premature.
Israel has long regarded the UN as a minor player in the Middle East peace process compared with the United States, which did not criticise the decision to withhold funds.
A day after Israel's cabinet announced a permanent halt to the monthly transfer of about $50 million in tax revenues Israel collects on behalf of the Palestinians, de Soto on Monday said: "These are monies that belong to the Palestinians and should not be withheld."
Israel's government made the decision after Washington, the Jewish state's biggest ally, asked the Palestinian Authority to return $50 million of its own aid to ensure it does not reach Hamas.
But de Soto said Israel's decision to withhold the money ran counter to the position taken last month by the so-called Quartet of major peace mediators - the United States, the European Union, the United Nations and Russia.
After Hamas's victory in a Palestinian parliamentary election on 25 January, the Quartet said foreign donors should continue to aid the caretaker government of Mahmoud Abbas, the Palestinian president, at least until Hamas formed a new administration.
"These are monies that belong to the Palestinians and should not be withheld"
Alvaro de Soto,
UN special envoy
De Soto said: "It follows that the formation of a new government and the approval of its programme should be awaited and that actions prior to that would be premature."
Israel has called on the international community to shun a Hamas-led government until it renounced violence, recognised the Jewish state and agreed to abide by all previously signed interim peace accords.
De Soto said Israel's obligation to transfer the tax revenue to the Palestinian Authority stemmed from one of these agreements.
"If the future Palestinian government has doubts about complying with previous agreements, these will be reinforced by non-compliance with those agreements by the other party to them," he said.
"The government's decision of yesterday stands"
Israel's Foreign Ministry spokesman
Mark Regev, Israel's Foreign Ministry spokesman, countered that it was Hamas which said "these agreements should be thrown on the ash heap of history".
"The government's decision of yesterday stands," he said.
Aides said de Soto relayed the UN's objections to Israeli defence officials at a meeting on Sunday.
The Palestinians receive about $1 billion a year from donors, and the Palestinian Authority requires at least $100 million a month.
De Soto said: "Depriving the PA (Palestinian Authority) of funds which are due to it at this time would not be helpful."