Lowdon told Reuters at the Mexican Grand Prix he could not comment on the reports about the departures, which the BBC said had been confirmed by 'sources close to the team.'
However, he said he and Booth would remain in charge of the tail-end team for the final three rounds of the championship.
The departure would be a major blow for the struggling team's prospects, with both men well regarded in the paddock.
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Mercedes motorsport head Toto Wolff said the pair were "real fighters who have shown stamina in keeping the team in the sport.
"I've known John forever, since the Formula Renault days of Lewis (Hamilton)," he added. "Manor means John Booth, and John Booth means Manor.
"And Graham was also very instrumental in keeping the team alive last year. So seeing them go from a personal standpoint and from the racing spirit is obviously a blow."
Manor are due to switch from year-old Ferrari engines to Mercedes power units next season and have yet to confirm any drivers. American Alexander Rossi and Britain's Will Stevens are the current lineup.
"I would say we need to give credit to everybody in the team who stays ... but we are curious spectators from now on," said Wolff.
Booth and Lowdon are founders of Manor, who competed in junior series before entering Formula One in 2010 as Virgin Racing.
The team were then transferred to Russian ownership, becoming Marussia, before hitting financial hard times and going into administration last year, missing the final three races.
Stephen Fitzpatrick, who runs the Independent British energy supplier Ovo, then took over as owner in March and has said he was funding the team personally.
Former Sainsbury's Chief Executive Justin King was appointed interim chairman.
The British-based team have not scored any points this season and are last in the standings.
However, they qualify for an estimated $50 million in prize money after finishing ninth last year thanks to the efforts of their late French driver Jules Bianchi, who suffered fatal injuries in Japan last year.
(Reporting by Alan Baldwin, editing by Toby Davis/Peter Rutherford)
