Two former leaders of the Boston Harbor Pilots Association, whose members guide massive container ships and tankers through Boston Harbor, have been charged with stealing from the group.

A Suffolk County grand jury has indicted Gregg Farmer, the association’s president from 2002 to 2011, and its former executive director, Andrew Hammond, on larceny charges, District Attorney Daniel Conley announced last week. Hammond was also charged with falsifying documents.

Conley spokesman Jake Wark said the pair are accused of using tens of thousands of dollars in pilot association funds “to pay for expenses wholly unrelated to their employment, such as personal taxes, car repair, fuel, and cellular service,’’ among others.

Hammond faces additional charges, including making false entries in corporate books to conceal evidence that he wrote checks to himself from the group. Prosecutors also said Hammond obtained a credit card for himself in the name of a corporation set up by the pilots.

The Globe reported in September 2016 that Farmer had been accused by his fellow pilots in a lawsuit of using the association’s credit cards to splurge on more than $100,000 worth of personal expenses — including fishing gear, luxurious vacations, and a $9,000 outing to a strip club that his attorney claimed was a necessary business expense because it boosted morale “during very strenuous times in the port.’’

Farmer’s attorney, Thomas Fallon, said all the expenditures his client made were approved by other members of the pilot’s association, and accused the group of prompting the criminal investigation in an effort to force Farmer out and divide his salary among the remaining pilots.

“To the extent they’re saying that Captain Farmer did this for his personal benefit only — and that it had nothing to do with the pilots association and they knew nothing about it — that’s contradicted by the fact that they had two pilots sign every check,’’ Fallon said. “Furthermore, the pilot’s association had stated to Captain Farmer a couple years ago that unless he resigned, they were going to go to [Conley’s] office and get criminal charges brought against him. Then you have eight other pilots who are going to share in $400,000 per year.’’

Hammond referred a request for comment to his attorney, who did not respond.

Tim Bradl, an attorney for the association, said the pilots are “grateful to the DA for beginning to unravel the scheme, and we look forward to [Farmer and Hammond] being held accountable in court.’’

The men are scheduled to be arraigned Jan. 25 in Suffolk Superior Court. A conviction for larceny can result in a prison sentence of up to five years, while the document-falsification charges against Hammond could each bring 10 years.

In 2016, the pilot’s association asked an obscure regulatory body that oversees the group, the Commissioners of Pilots for District One, to strip Farmer’s maritime license over the alleged misuse of funds.But the tiny agency refused, saying it had jurisdiction only over conduct related to Farmer’s duties at sea. A lawsuit brought by the pilots seeking to compel the commissioners to act was dismissed by a state judge last year.

In response to the complaint to the commissioners, Farmer submitted a series of salacious counter-allegations.

One pilot, Farmer said, routinely drank alcohol at the association’s headquarters on the East Boston waterfront while waiting to be assigned to an incoming or outgoing ship. He accused another of failing to appear when he was supposed to be available to move a docked tanker containing liquid natural gas in case of an emergency. And, Farmer said, that same pilot belittled a State Police trooper over marine radio, angrily threatened a state legislator, and once used his phone to bid in an online auction for NASCAR memorabilia while steering a large ship through a narrow channel.

The commissioners, saying they had received no complaints from others on the harbor and that none of the pilots had failed random drug or alcohol tests, concluded Farmer’s allegations were either “hearsay’’ or matters to be resolved internally by the harbor pilot association.

The association at the time said its members had piloted nearly 20,000 ships without incident since 2006, and insisted the public was safe.

Dan Adams can be reached at daniel.adams@globe.com. Follow him on Twitter @Dan_Adams86.