Government is not biased to The New Age newspaper in its adverting spending, the presidency said on Thursday.
"Government undertakes advertising in all mediums across the board, which reaches a variety of targeted audiences," it said in a statement.
"The government advertising is spent in newspapers across the country, radio stations, television and digital media. In this regard, there is no basis for accusation of advertising bias towards The New Age newspaper."
On Wednesday, Democratic Alliance leader Helen Zille called for a commission of inquiry to probe funding of TNA.
She said the newspaper was almost entirely funded with taxpayers' money, and claimed 77 percent of its advertising revenue came from national and provincial government departments, and state entities.
She drew parallels with the apartheid-era scandal involving The Citizen, in which state money was used to set up and fund the newspaper.
In the financial year 2012/2013 government had by end of November 2012 through Government Communication and Information System (GCIS) media bulk buying, spent R108-million across all media platforms.
A total of about R17-million of public funds was saved, the Presidency said.
The advertising expenditure on groups of newspapers for the past two financial years through GCIS was R20-million in 2010/2011, R55.8-million for 2011/2012 and R59.3-million in the current financial year.
This excluded direct advertising by departments, provinces, municipalities and state-owned entities that do not work through GCIS.
In the 2010/2011 financial year R7-million (52 percent) was spent on the Naspers group of newspapers.
A total of R6.9-million (34 percent) was spent on Avusa media (now called Times Media Group) and R2.7-million (13.6 percent) on Independent Newspapers.
Government spent only R122 700 (0.6 percent) on the TNA newspaper.
In the 2011/2012 financial year, R19.4-million (35 percent) was spent on Naspers while R15.6-million (28 percent) was spent on Avusa media.
A total of R7.9-million (14 percent) was spent on Independent Newspapers and R8.9-million (15.9 percent) on the TNA.
In the current financial year the advertising spent was R16-million (27 percent) on Naspers, R16.5-million (28 percent) on Avusa, R11.7-million (19.7 percent) on Independent Newspapers and R6-million (10.2 percent) was spent on TNA.
"This analysis states clearly that The New Age newspaper enjoys less advertising as compared to other groups of newspapers."
The presidency said the DA's conclusion was therefore unjustified.
Zille's spokesperson Cameron Arendse said the Presidency had missed the point.
"In fact, more than 77 percent of their [TNA] revenue is from government advertising. They are also the only paper receiving millions in so-called 'sponsorship' from government."
He said the ANC government and TNA had systematically attempted to divert attention away from the key issue in this debate.
"The fact that TNA received R64.6-million in less than two years and that it is sympathetic to government, the President clearly fears what the investigation would reveal," Arendse said.