Die Welt newspaper reported that Infantino had improperly ordered the destruction of the minutes of a FIFA executive committee meeting held at last month's congress in Mexico city.
According to the paper, FIFA's independent ethics committee was looking at the issue and could impose a 90-day ban on the new president if the allegation was confirmed.
But a spokesman for the ethics committee's investigatory arm, Roman Geiser, told AFP that "there are no formal proceedings going on against Mr. Infantino".
FIFA spokeswoman Delia Fischer, in a separate statement emailed to AFP, said the allegations were baseless.
"This mention does not refer to the officially archived audio file. That file exists and is properly saved at FIFA."
The volatile Mexico City congress was the first since Infantino replaced FIFA's disgraced former president Sepp Blatter following a vote during an extraordinary congress in Zurich on February 26.
It included the shock resignation of FIFA's audit and compliance chief Domenico Scala, who accused Infantino of trying to compromise the independence of key FIFA bodies, including the ethics committee.
Infantino, who has been in his new job for less than 100 days, has not yet agreed to a contract.
He has been widely criticised in the German press for allegedly refusing the salary proposed -- reportedly more than a million euros -- because he considered it insufficient.
Die Welt claimed Infantino had asked in emails to have the tape recording of the meeting in Mexico City, in which his salary was discussed, deleted.
