"Dissent in the ranks is wrong, there's nothing at all," Captain Ibrahim Traore said in a report by RTB state TV.
Traore, who came to power in an October 2022 coup, spoke at the grounds of the state-run television network where a rocket fell on June 12.
"Wanting to check a number of things, unfortunately someone fired the shot," a presidency statement quoted Traore as saying.
"The rocket headed into the courtyard of the RTB," he added, calling it an "incident".
Traore also attacked Western media, describing them as "lying" and "manipulators".
"Don't listen to 'fake news'. We are here and continue to work for the well-being of the Burkinabe people," he said.
After the visit, Traore chaired a cabinet meeting, the presidency announced on Facebook.
On Tuesday, the army slammed what it called unfounded and false "rumours on social media" of "dissent" in the ranks and mutinies in some barracks.
The remarks also follow a deadly jihadist attack in the northeast of the insurgency-hit country.
On June 11, an Al-Qaeda-affiliated group attacked the region of Mansila and a military contingent located near the border with Niger.
No official toll has been given but according to a security source many people are thought to have died.
In his first comments on the attack, Traore said Thursday that an operation was launched in Mansila the day after the attack, with back-up troops sent to "mount the assault".
The junta chief also said six Russian military planes had landed in the capital, Ouagadougou, with "equipment from the United Nations" coming from Mali.
According to an African diplomatic source and an independent source, the planes also brought a few dozen Russian instructors.
After taking power, the West African country's coup leaders expelled troops and diplomats from former colonial ruler France and have turned to Russia for military assistance.
For nearly 10 years, Burkina Faso, like neighbouring Mali and Niger, has been grappling with jihadist attacks that have killed more than 20,000 people and displaced two million.
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