On 24 March 2016, he was appointed for the sixth year running as the United Nations Special Rapporteur on the human rights situation in the Islamic Republic of Iran.

[9] On 13 June 2016, Shaheed was nominated by the Consultative Group of Ambassadors comprising Albania, Brazil, Egypt, France and Thailand, as the most suitable candidate to be appointed by the President of the Human Rights Council for the post of United Nations Special Rapporteur on Freedom of Religion or Belief, to succeed Professor Heiner Bielefeldt of Germany.

[13] At the end of 2003, Shaheed retired from the diplomatic service and took up a position in the President's Office mandated to formulate and coordinate political and human rights reform and government communications following outbreaks of civil unrest in the capital and nearby areas.

[14] In July 2005, Shaheed used his position as Government Spokesperson to reject the condemnation of the Universal Declaration of Human Rights by the Chief Justice of the Maldives.

[19][20] Shaheed offered "unconditional support" for the candidature of the opposition candidate, Mohamed Nasheed, in the run-off, and was appointed as his Foreign Minister when the latter won the presidency in October 2008.

[25] His resignation followed his open criticism of the parliament for having failed to protect the people's fundamental rights and for being a rubber stamp to sustain the 30-year-old rule of President Gayoom.

His second stint as Foreign Minister was no less controversial than the first, coming under fire from the parliament and radical Islamist parties for recognition of Kosovo as an independent State,[28] the development of cooperation with Israel[29] and the participation in the US programme to close down Guantanamo Bay detention facility by agreeing to relocate persons released from Gitmo.

[34] Earlier, from 1997 to 1998, Shaheed had served as a member of the Group of Eminent Persons mandated by the leaders of the South Asian Association for Regional Cooperation, comprising Afghanistan, Bhutan, India, Maldives, Nepal, Pakistan and Sri Lanka,[12] while from 2009 to 2010 he served on the Commonwealth Ministerial Action Group mandated to oversee the protection of democratic values and human rights in the 54 member association of former British colonies.

However, for the first time since 2011, the Maldives, with Abdulla Yameen as president, refused to back Shaheed's re-appointment in 2014 as UN envoy, despite public appeals from Iranian civil society.

[38] In September 2013, he stirred considerable animosity from President Yameen when he called for international intervention to facilitate presidential elections[39] when the first round was nullified by the Supreme Court of Maldives.

[42][43] Living in self-imposed exile since the coup d'état of February 2012, Shaheed has been a vociferous campaigner for the restoration of democracy and for the advancement of human rights in Maldives.

[44] He has also been active on the international stage advocating human rights protection in Islamic societies, supporting freedom of religion and the abolition of the death penalty.