In February 1979, Nathan returned to the Foreign Ministry and became its First Permanent Secretary until February 1982, when he left to become the Executive Chairman of the newspaper company the Straits Times Press. The appointment was viewed dimly by journalists who felt that the Government was trying to limit freedom of the press; they wore black armbands in protest. According to Nathan in a 2010 interview, " When they saw I was not doing what they expected me to do, they began to have confidence." At various times between 1982 and 1988, Nathan also held directorships of several other companies, including the Singapore Mint, The Straits Times Press (London), Singapore Press Holdings and Marshall Cavendish. He held a directorship in the Singapore International Media between September 1996 and August 1999. He was Chairman of Mitsubishi Heavy Industries Singapore, a ship-repairing and engineering joint venture with the Mitsubishi Group of Japan, from 1973 to 1986. From 1983 to April 1988, Nathan was Chairman of the Hindu Endowments Board. He was a founding member of the Singapore Indian Development Association (SINDA), and its term trustee until August 1999.