The probe is financial in nature and apparently targets the fire chief, the chief said.
Fire Chief Paul Perrotti said he got a call from the FBI at 8 a.m. saying agents were at the fire station at 65 Tucker Hill Road. He answered some questions and allowed them full access, he said.
The agents were looking for any information about payroll, Perrotti said.
"I figured, by no means have I done anything wrong," he said in a telephone interview shortly before 2 p.m. "I gave them full transparency."
Perrotti runs a volunteer fire department with some 100 members. He earns a stipend that adds up to about $600 a month, he said.
"I think somebody's got an ax to grind," he said. He didn't know who that would be, he said.
Perrotti says he believes someone made a complaint about the fire department misappropriating funds.
"It was important to say there is nothing going on like that. This is a complaint that is a baseless complaint," Perrotti said.
The FBI declined to talk about the investigation.
"All I'm prepared to say is FBI agents were in Middlebury, Connecticut, this morning working in support of an investigation," spokesman Dan Curtain said.
Middlebury town officials say a recent audit showed no irregularities with the funding the town gives to the department, which includes Perrotti's $600 monthly stipend.
The Department allocated around $300,000 to the volunteer fire department in this year's budget, but the department has its own private account for expenses, and equipment purchases, which the chief has full control over without any town oversight.
"We fund much of their department, but there is a portion we don't fund called: Middlebury Volunteer Fire Department, Inc.," said Middlebury First Selectman Edward St. John.
St. John, a former Middlebury Volunteer Fire Department chief in the late 1960s, says he had no reason to suspect any wrongdoing. Middlebury town officials say they have not been contacted by federal agents regarding the investigation.
"Hopefully, whatever this investigation ultimately reveals or doesn't reveal, the department has our support," St. John said.
Middlebury is a town with about 7,000 residents, and some of those residents were stunned by Thursday's developments..
"I'm shocked. There wasn't any foreboding that anything was going or gave us a tip that anything was going on inappropriate," said Middlebury resident Thomas Carroll.
Chief Perrotti is the owner of Perrotti Electric, L.L.C., but he says there was no link between the company and operations at the fire department.