Lotito said Serie B leaders Carpi were "not worth a cent" before the club replied that he had offended their dignity.
Italian football federation (FIGC) president Carlo Tavecchio then told his organisation's website that promotion and relegation would be decided purely on results.
"Promotion and relegation are decided by results on the pitch and only by that. There cannot be, and are not, calculations of any other kind," he said.
La Repubblica published the text and an audio recording of the phone call, saying it was between Lotito and Pino Iodice, a director of third tier Ischia Isolaverde.
Lotito is one of the most outspoken presidents in Italy and last year said he had received more than 50 death threats after the club sold midfielder Hernanes to Inter Milan at the end of the January transfer window.
"Do you, by any chance, think Beretta decides anything in Serie A?", said Lotito. "Do you know what he decides? Nothing."
He then turned to Carpi, a small team who have climbed the lower divisions to lead Serie B and are poised to reach the top flight for the first time.
DONE WELL
"If Carpi come up ... if teams come up who are not worth anything in lira, in two or three years we won't have a lira," said Lotito.
"I’ve done well in selling television rights, we brought in 1.2 billion euros ($1.37 billion) thanks to my ability.
"If in three years we have Latina, Frosinone, who would buy those rights?" he said, referring to two other unfashionable Serie B teams. "They don't even know where Frosinone is."
Carpi said Lotito's remarks were "completely inappropriate and out of place".
"Like it or not we exist and, yes, we are a provincial club who have won four championships in five seasons, starting out among the amateurs," the club added.
Lotito later explained his comments as he spoke to reporters in Milan.
"The system is wobbling, this is an undeniable fact and comes from someone who, it has been shown, understands the accounts," he said. "The situation is dramatic because we don't have the resources.
"In relation to Beretta I simply said he has no power. He is there to oversee, it is the assembly that matters."
(Writing by Brian Homewood, editing by Tony Jimenez)
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