Naidu opposed the 2006 Fijian coup d'état as illegal and unconstitutional.^[11] He condemned the detention and beating of six pro-democracy activists by the military on Christmas eve at the Queen Elizabeth Barracks, and called on the Fiji Human Rights Commission to take a stand against such violations. Naidu also spoke out against the Fiji Human Rights Commission for supporting the coup, ridiculing a report written by the Commission's Director, Shaista Shameem, which endorsed the coup.^[12] On 16 January, Naidu dismissed the announcement that the Military had restored Ratu Josefa Iloilo to the Presidency, saying that it did not legitimize the State of Emergency or the interim government.^[13]

On 23 January Naidu gave an interview to Radio New Zealand in which he attacked President of Fiji Ratu Josefa Iloilo as a puppet of the Military and the "illegal" interim government.^[14] He was also quoted as accusing the interim government of making "illegal laws" ad hoc to circumvent court rulings it did not like.^[15] He was subsequently arrested by the military and taken to Queen Elizabeth Barracks for interrogation.^[16] He was released after intervention from military Attorney-General of Fiji Aiyaz Sayed-Khaiyum^[17][18] and Human Rights Commissioner and Fiji Women's Crisis Centre coordinator Shamima Ali.^[19]

Following the coup, Naidu represented opponents of the regime, such as Fiji Law Society vice-president Tupou Draunidalo and the Fiji Times.^[20][21] In May 2009 he was detained and his computer was searched on suspicion he was involved with an anti-military blog site.^[22][23] In June 2009 he withdrew from speaking at Fiji's Institute of Accountants Congress after threats from police.^[24] He later criticised the military regime for denying a permit for the Fiji law Society's annual general meeting.^[25]

Naidu later worked as the editor of the FijiLive website. In July 2010 he was detained by the military under the Media Industry Development Decree 2010 over an article claiming the Fiji police commissioner had been suspended.^[26][27]

In 2015 he briefly served on the Constitutional Offices Commission as the leader of the opposition's nominee,^{[28][circular reference]} resigning in November after claiming it was a rubber-stamp for the regime.^[29] He later criticised the government's proposed Parliamentary Powers and Privileges Bill and Code of Conduct Bill for undermining freedom of speech.^[30][31]

In November 2022 he was convicted of contempt of court after pointing out a spelling mistake in a judicial judgement in a Facebook post.^[32][33][34] The conviction was condemned by Amnesty International,^[35] the Commonwealth Lawyers Association,^[36] the New Zealand Law Society,^[37] the Law Council of Australia,^[38] and legal academics.^[39] In July 2023 the court set aside the conviction and dismissed the charge.^[40]