In a statement on Monday, the ministry announced the expiration of Manyi's contract after serving his full three-year contract.
"Mr Jimmy Manyi was very instrumental in communicating government programmes, particularly the five priorities of government to the people of South Africa. He has made a good contribution to government communication and Cabinet communication processes. On behalf of the president, Cabinet and government I would like to thank Mr Manyi for his contribution to government communication" said Minister for Performance Monitoring and Evaluation Collins Chabane.
Political analyst Adam Habib told the Mail & Guardian that Manyi had left one of the worst legacies as a government communicator.
"He had a controversial tenure as head of the GCIS. He alienated Cabinet ministers and made provocative statements. Instead of conveying government news he became the subject of news. That's not what you want from the head of the GCIS. He did not do as well as he could have," said Habib.
The M&G has been reliably told that Home Affairs spokesperson Ronnie Mamoepa is tipped to succeed Manyi as the GCIS CEO.
Political analyst Zamikhaya Maseti added that Manyi, a geologist by profession, had little understanding of how government communications functioned – including how to observe protocol.
"His abrasive style of communication was his biggest downfall," said Maseti.
"He did not observe government protocol if you look at the incident in which he had used an official meeting with Norwegian diplomats to solicit business on behalf of an associate."
"I really do not think he was ready for the position. Manyi's appointment as GCIS CEO also brings to question the deployment strategy of the ANC. He might have mobilised the Black Management Forum behind President Jacob Zuma election after Polokwane but he did not have the requisite skills to head the GCIS. Those who were behind his appointment must now take the blame for the poor state of the GCIS and its hostile relationship with the media under his leadership," said Maseti.
Manyi joined the Government Communication and Information System (GCIS) in February 2011 from the labour department where he was transferred to complete the rest of his contract as director general in the public service.
Deputy chief executive officer of corporate services Phumla Williams has been announced as his acting replacement until the position has been filled.
Last week, the M&G reported that Manyi suffered a double blow when the treasury rejected his plans for restructuring the government communications agency.
And the presidency slammed the controversial government spokesperson's lack of consultation.
Since joining the communications agency in February last year, Manyi has been tinkering with structural changes, but was stopped in his tracks by the treasury.
Before former GCIS chief executive Themba Maseko left, he conducted a review of the organisation with a new organogram. But when Manyi joined, he introduced another structure, upsetting some people in the government.
"There is a concern that it appears that your department is preparing itself for growth during a constructive climate and the baseline impact of this structure change needs to be interrogated in more detail," Manyi was told in the letter, written by Japie Jacobs, director general of government and administration in the treasury.
Jacobs added: "There are two new sub-programmes that your department wants to introduce in 2013-2014, namely cluster supervisor [human development, social protection and government and administration] and cluster supervisor [economic and infrastructure, justice and international]. Introducing these sub-programmes suggests a requirement for additional staff and other related resources, for which there is no guarantee that additional funding will be received."
Jacobs said the GCIS had previously indicated its budget pressures and how it had had to reprioritise to accommodate some of its main goals, impacting on staff morale and resulting in high staff turnover. "Based on this, it does not seem possible that these additional sub-programmes will be funded internally, except through additional funding."
The M&G understands that Manyi also did not get approval for his plans from Collins Chabane, the minister in the presidency responsible for performance monitoring and evaluation.
On Thursday, the M&G was shown another letter from the presidency signed by Chabane's deputy, Obed Bapela, in which he warned Manyi about going ahead with his restructuring plans.
"As the deputy minister delegated to provide ministerial oversight and responsibility to the GCIS, I hereby appeal to the top management not to proceed with the planned restructuring of the institution," Bapela wrote.
"It is my firm belief that the restructuring of the GCIS should be holistic and not piecemeal. When the transition phase has been completed, the GCIS, in consultation with the executive authority, will engage on the process that will be followed in restructuring the institution. The restructuring process should be done in a holistic manner, with a view to shape the institution to respond to current demands and needs of the ruling party [the ANC]."
When approached for comment by the M&G, Manyi retaliated by issuing a statement titled "Smear campaign against Manyi orchestrated through the Mail and Guarian [sic]" and rejected claims that he had not informed Chabane about his restructuring plans.
"Any insinuation that the minister may not be aware is simply a misunderstanding of the collective decision-making processes of Cabinet or undermining the authority of the minister in GCIS operations," said Williams in the statement.
"Our request was in no way for funding or a restructuring of the organisation, but for the name changes of the branches in compliance with the national treasury guidelines," said Williams.
A government official told the M&G: "The man has been changing the structure, moving people and renaming sections and units ad infinitum. Whereas his predecessor, Joel Netshitenzhe, left some degree of intellectual depth in government communications, Manyi mistook abrasiveness and aggression for intellectual sophistication."
The official added: "Maseko had a good relationship with the media, but Manyi came in and destroyed that through his confrontational approach. He leaves no tangible legacy behind except an unstable GCIS and strained relations with the media and government communicators in general. He will be remembered for all the wrong reasons."