From 2008 to 2009, during the 2009 general election campaign, he worked at Luthuli House as the head of the ANC presidency under Jacob Zuma.

President Cyril Ramaphosa promoted him to the cabinet on 5 August 2021 following the resignation of the former Health Minister, Zweli Mkhize.

[5] In 1982, he told the Christian Science Monitor that one of his priorities as AZASO president was to establish closer ties with community and labour organisations.

[11] At the next provincial party elective conference in 1998, Phaahla ran to succeed Mashamba but was defeated by Ramathlodi, who returned to the chairmanship.

[1] In August 2005, Phaahla was appointed to a three-year term as director-general in charge of the government unit that coordinated South Africa's preparations for hosting the 2010 FIFA World Cup.

[13] In January 2008, he asked to be relieved early from his contract as director-general in order to pursue opportunities in the private sector and dedicate more time to party-political work.

His candidacy had been endorsed by the Congress of South African Trade Unions (Cosatu),[14] and he received 1,726 votes from the roughly 4,000 delegates at the conference, making him the 40th-most popular of the 80 ordinary members elected to the committee.

[3] During his tenure in the Arts and Culture Ministry, in 2011, Phaala launched a campaign to succeed Premier Cassel Mathale as the Provincial Chairperson of the Limpopo ANC.

[21] Their ticket was reportedly supported by the provincial branches of Cosatu and the South African Communist Party, as well as by President Zuma's faction of the national ANC.

[21][22][23] Indeed, the outcome of the race was viewed as important to Zuma's re-election bid at the ANC's 53rd National Conference, with Adam Habib and others believing that "If Phaahla wins, Limpopo will be in the president's hands.

[27] Phaahla himself said later that week that he accepted his defeat,[28] but his supporters – reportedly led by Falaza Mdaka[29] – launched a formal complaint with ANC Secretary-General Gwede Mantashe, claiming that some of the votes had been invalid.

[30] The national ANC appointed a task team, led by Jeff Radebe, which was unable to find evidence to substantiate the complaint.

[31] He was also touted as a possible candidate to serve as Premier of Limpopo after Mathale was removed from the office in 2013,[32] though that position ultimately went to Stan Mathabatha.

[33] Over the next four years, and amid the political controversy that surrounded Zuma's second term, Phaahla became reputed as a relatively outspoken critic of the president.

[34] During ANC National Executive Committee meetings, he reportedly supported both of two motions of no confidence lodged against Zuma in his capacity as party president, one tabled by Derek Hanekom in November 2016[35] and another tabled by Joel Netshitenzhe in May 2017;[36] on the latter occasion, Phaahla reportedly raised the ANC's poor performance during the 2016 municipal elections as a reason that Zuma should be removed from office.

[41] The Treatment Action Campaign welcomed the departure of Mkhize and the appointment of Phaahla, who it said had "ably served as a deputy minister".

[2] Phaahla took office during the third wave of COVID-19 infections in South Africa,[4] and his first task was to oversee the roll-out of COVID-19 vaccines to the public.