In the same year, he was appointed head of the newly established Department of External Affairs, the precursor to the Ministry of Foreign Affairs. He accompanied Fraser to the Australia–New Zealand meeting in January 1944 and later that same year to the 1944 Commonwealth Prime Ministers' Conference in London. McIntosh was a senior member of the New Zealand delegation to the San Francisco Conference in 1945, which was to lead to the establishment of the United Nations.
In that same year, he took charge of the newly formed Department of External Affairs, predecessor to the Ministry of Foreign Affairs. He joined Fraser for the Australia–New Zealand meeting in January 1944 and later attended the 1944 Commonwealth Prime Ministers' Conference in London. McIntosh was a key figure in the New Zealand delegation at the San Francisco Conference in 1945, which resulted in the creation of the United Nations.