Macron has said he intends to keep his distance from the press in an effort to restore the authority of the presidential office.
Representatives from 25 media organisations including AFP, news channels BFM and TF1 and newspapers Le Monde and Le Figaro signed an open letter Thursday expressing their "concerns" about Macron's communication strategy.
"It is not at all up to the Elysee to choose who among us has the right to cover a trip, whatever the theme," the letter said.
Presidential spokesman Sylvain Fort said that "in one or two cases" journalists had been contacted directly and offered some of the limited places available to travel with Macron to Mali on Friday.
Other aides had previously described the choice of journalists as a deliberate ploy to bring along "specialists" rather than the political media pack which routinely follows the president.
"The journalists who were worried can be reassured: the Elysee does not intend to do the work of newsrooms," said a statement from the presidency addressed to media freedom group Reporters without Borders, which also signed the open letter.
Macron, 39, has said he intends to keep his distance from the press in an effort to restore the authority of the presidential office which he felt was damaged under his gossip-loving predecessor Francois Hollande.
Hollande would regularly chat to reporters off-the-record but was damaged by a tell-all book, "A President Shouldn't Say That", published at the end of his term based on his conversations with two political journalists.
A regular in glossy magazines during his political ascent and omnipresent on television during campaigning, Macron now plans to speak rarely in an effort to keep focused on his longer-term priorities.
Journalists were cleared out of the presidential palace press room soon after his inauguration last Sunday and were kept at a distance during the first meeting of his government on Thursday.
Government spokesman Christophe Castaner told a press briefing on Thursday that ministers were also under strict instructions not to leak to the media.
The first government is a melting pot of figures from centre-right, centrist and Socialist parties as well as newcomers to politics, which some observers believe could lead to tensions and differences over policy.