The west African country has seen several military takeovers in its history and spent much of the 20th century under junta rule since its independence from Britain.
A fresh coup would turn back the clock on more than a quarter century of civilian rule.
"The Armed Forces of Nigeria (AFN) wishes to categorically state that the claims by the said publication are entirely false," said a statement from Tukur Gusau, director of defence information, without specifying which outlet he meant.
But Sahara Reporters, an online publication, and Premium Times, based in the capital Abuja, both said Saturday that at least 16 officers were planning to overthrow President Bola Tinubu.
The military had announced earlier this month that 16 officers had been arrested over "issues of indiscipline".
The two media outlets, citing defence sources, reported that the arrests were in fact linked to a coup plot.
The military is fighting a long-running insurgency against Boko Haram and Islamic State West Africa Province in the northeast.
While the violence has waned since its peak a decade ago, attacks continue -- including deadly assaults on military bases -- seemingly with no end in sight.
Analysts have warned of a rise in jihadist violence this year, while troops have at times reported unpaid wages and poor conditions.
The military is stretched thin on other fronts as well, including fighting armed gangs known as "bandits" in the northwest and separatists in the southeast.
Earlier this month, the army announced that "a routine military exercise has resulted in the arrest of sixteen officers over issues of indiscipline and breach of service regulations".
The statement added: "Investigations have revealed that their grievances stemmed largely from perceived career stagnation caused by repeated failure in promotion examinations, among other issues."
In Saturday's statement, Gusau said the investigation was "a routine internal process aimed at ensuring discipline and professionalism is maintained within the ranks".
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