[1][2] In September 1995,[1] President Nelson Mandela appointed Baqwa as the inaugural Public Protector, an ombudsman position established under Chapter Nine of the post-apartheid Constitution.
Many commentators agreed with Baqwa that the Public Protector was severely under-resourced,[4][5] complimenting the administrative prowess he demonstrated establishing the office in that context.
[6][7][8] However, some commentators questioned the extent of Baqwa's independence from the ANC government, with Richard Calland saying that he was careful "not upset too many political apple carts too early in the life of a new institution".
[6] He was criticised in particular for his putatively lenient treatment of ANC politicians in the Public Protector's investigations into the Sarafina II and Arms Deal scandals.
[7][9][6] He was nonetheless lauded for making adverse findings against Premier Ndaweni Mahlangu and Minister Penuell Maduna in two highly publicised scandals in 1999;[6][7] his report in the Mahlangu matter was strongly rejected by the ANC majority in the Mpumalanga Provincial Legislature,[10] and his report in the Maduna matter was rejected by the ANC majority in the National Assembly.
[14] In April 2001, Noseweek reported that Baqwa, Judge Fikile Bam, and prosecutor Bulelani Ngcuka had attended a secret meeting at the home of ANC Chief Whip Tony Yengeni, where attendees had discussed ongoing investigations into Arms Deal corruption.
[21] Baqwa remained at Nedcor (renamed Nedbank) until July 2011, when he accepted appointment as an acting judge of the Gauteng Division of the High Court of South Africa.
[25] Presiding in the Pretoria High Court, Baqwa heard two high-profile matters relating to the assassination of Chris Hani:[26] in September 2018, he overturned Justice Minister Michael Masutha's decision to deport and refuse parole to assassin Janusz Waluś,[27] and before that, in a separate matter in May 2015, he granted medical parole to Waluś's accomplice, Clive Derby-Lewis.
[28][29] In January 2013, Baqwa was among five candidates – the others being Ronnie Bosielo, Brian Spilg, Jeremy Gauntlett, and Mbuyiseli Madlanga – who was nominated for possible appointment to retired justice Zak Yacoob's seat in the Constitutional Court of South Africa.