Less than two hours after Secretary-General U Thant learned of Egypt's intention to seek UNEF's withdrawal, he met with Muhammad al-Kony, the permanent representative of the UAR to the UN. Unaware what was happening back home, al-Kony was told by U Thant that there had, in effect, been a breach in protocol and that any request for the removal of UNEF must be directed to the secretary-general. U Thant also sought clarification of Nasser's intent. The original note only made mention of withdrawing from the outposts along the UAR border, yet in the course of the discussion with General Rikhye, specific mention had been made of withdrawing from the UN positions at Sharm al-Shaykh and al-Sabha. It was also unclear whether the withdrawal was of a permanent or temporary nature.

In the view of the secretary-general, however, a temporary withdrawal "would be unacceptable because the purpose of the UN Force in Gaza and Sinai is to prevent a recurrence of fighting, and it cannot be asked to stand aside in order to enable the two sides to resume fighting."[14] While seeking this clarification, U Thant sought to reassure Ambassador al-Kony that were the UAR government to withdraw its consent for UNEF's presence on their territory, the secretary-general would be obliged to respect their wishes. U Thant did not think that this position required consultation and made it clear from the start that any request for a temporary withdrawal or redeployment of UNEF's forces would be considered as a call for the entire UN force to leave.