"What we know is that these actions have been taken against individual people, not against the institution," current FEPAFUT president Pedro Chaluja told reporters.
Alvarado, who headed the Panamanian football body FEPAFUT between 2000 and 2011, is a current member of FIFA's disciplinary committee.
"The Panamanian Football Federation has not been contacted by anybody and is not under any type of investigation. We don't know the details of all that has been put out there," Chaluja added.
FEPAFUT put out a statement saying it believed the accusations against its former boss had to do with "a bribery case involving in a personal and direct way Mr Ariel Alvarado and the Traffic company."
That referred to Traffic Group, a Brazilian-based company that handles marketing rights for football events. The group's owner, Jose Hawilla, pleaded guilty a year ago to racketeering, money laundering and wire fraud.