With the results of the referendum, the states of Malaya, Singapore as well as the crown colonies of North Borneo and Sarawak merged to form the Federation of Malaysia.

The union would prove tenuous due to various factors, and would end up lasting for just one year, ten months and 24 days before Singapore ultimately became a fully sovereign country.

The Council of Joint Action (CJA) founded by 19 members of the Assembly[b] to block the merger and scuttle the referendum by taking the issue before the UN Committee on Colonialism.

On 6 July 1962, The CJA signed a memorandum condemning the referendum on the grounds that the proposed constitutional changes and to assure its continued right to bases in Singapore, and to protect its privileged economic position.

In the memorandum, The CJA concluded that the transfer of sovereignty would be contrary to the spirit and resolution of the United Nations General Assembly's Declaration on the Granting of Independence to Colonial Countries and Peoples.

Backed by the official mandate, the Agreement relating to Malaysia between the United Kingdom of Great Britain and Northern Ireland, Federation of Malaya, North Borneo, Sarawak and Singapore was signed on 9 July 1963.