The move would further worsen the humanitarian crisis facing Palestinians, Guterres warned, according to his spokesman Stéphane Dujarric.
"This announcement comes on top of earlier restrictions that have already delayed critical food, medical, hygiene and shelter supplies from entering Gaza. This recent action will further exacerbate the humanitarian crisis facing Palestinians," Dujarric said in a statement.
Israeli authorities demanded aid groups register from January 1, a requirement many organisations reject as unlawful.
According to the Israeli Ministry of Foreign Affairs, they must cease their activities by March. This also affects operations in the Gaza Strip, largely destroyed by the war between Israel and the Palestinian Islamist militia Hamas.
A total of 37 organisations are affected, including Doctors Without Borders (MSF) and Oxfam.
In a joint statement issued by Oxfam on behalf of 53 international non-governmental organisations, the groups called on Israel to "immediately halt deregistration proceedings and lift measures obstructing humanitarian assistance."
"We urge donor governments to use all available leverage to secure the suspension and reversal of these actions," the statement added.
Israel's threat to deny registration to aid groups is "a cynical and calculated attempt to prevent organisations from providing services in Gaza and the West Bank," Doctors Without Borders said in a separate statement, adding that Israel was violating its obligations under international humanitarian law.
The Israeli Ministry of Foreign Affairs stated the registration is intended "to prevent the involvement of terrorist elements and to protect the integrity of humanitarian work."
Critics, however, say there are unclear regulations in the Israeli registration requirements for international aid organisations, which allow for arbitrary decisions.
Organisations are also reportedly required to disclose confidential information about Palestinian employees and to dismiss staff upon request without being given reasons.
The involvement of a party to the conflict in personnel checks is seen as a violation of humanitarian principles such as neutrality and independence.
Offers for review by neutral bodies have so far been rejected.
with DPA
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