Verizon Communications Inc. has paid the state of Massachusetts $1.3 million to settle charges that it overbilled the state for phone service.

The settlement came after an investigation by Massaschusetts Attorney General Martha Coakley's office that found Verizon had overcharged agencies and cities from 2006 to 2012. The settlement was not filed in court.

Under the terms of the settlement, state and municipal agencies may be eligible to receive additional payouts from Verizon. The largest overcharge allegedly was applied to the MBTA, which paid $52,000 in excess payments. Most agencies, including school districts and social service providers, allegedly were overbilled by amounts at or below $10.

Verizon did not admit or deny wrongdoing as part of the settlement.

"After a thorough review, Verizon and the attorney general have agreed to settle certain billing issues under a now-expired state contract," said Verizon spokesman Phil Santoro. "We have a long history of providing reliable, cost-efficient services and promptly addressing issues that can arise under agreements as complex and wide-ranging as the state’s blanket contracts."

Coakley's office began investigating the company after a whistleblower filed suit against Verizon separately under the False Claims Act. The case involved the carrier overcharging bills on federal contracts. That lawsuit alleged that between September 2006 and October 2012 Verizon’s New England unit charged landline consumers, who were on state contracts, a rate higher than the one permitted by the state.

Verizon in the past few months has settled other complaints concerning overcharging consumers. In November, Verizon was charged $1.4 million for deceptive marketing practices and misrepresenting charges for Maryland FiOS users. In October, Verizon paid $64.2 million for overcharging on its Family Share Plan.

In 2010, Verizon paid a $25 million fine, along with $52.8 million to give refunds to users who had been improperly billed. The company previously paid $90 million for unlawfully charging users for Internet access.

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