Merck & Co. has agreed to pay $24 million to the state Medicaid program to settle long-running civil charges that it charged too much for some drugs, in the largest single-case Medicaid fraud settlement in Massachusetts history.

The agreement, unveiled yesterday by Attorney General Martha Coakley’s office, closes out a 2003 lawsuit filed against 13 drug makers over inflated prices for medicines that were sold in pharmacies.

The state previously recovered a total of $23.4 million from the other 12 companies involved, but Merck, the nation’s second-largest drug maker, appealed a US District Court ruling last year in favor of the state. Its decision to settle brings the entire case to a close.

Coakley said her office’s Medicaid fraud division wanted to hold accountable drug companies that defraud taxpayers. The state could have accepted $1.5 million to $2 million two years ago as part of a settlement of a related federal case against Merck, but it chose to press its own case against the Whitehouse Station, N.J., company.

“We felt we had the ammunition and it was important that we push forward with this case,’’ Coakley said. “Companies will charge what they can as long as they feel they can get away with it. We’re going to keep a tight watch on how taxpayers’ money is spent.’’

The state’s eight-year-old complaint against the 13 companies accused them of knowingly submitting inflated prices to price-reporting services between 1995 and 2003.

Initially, the suit named Warrick Pharmaceuticals Corp., a generic drug unit of the former Schering-Plough Corp.; it was bought by Merck for $41 billion in 2009.

Ron Rogers, a spokesman at Merck corporate headquarters, said the drug company did not admit liability or wrongdoing in the settlement. He said Merck agreed to resolve the claims to put the matter behind it.

“We believe that settlement of the Massachusetts case is in the best interests of the company because it eliminates the uncertainty of ongoing litigation,’’ Rogers said.

The suit alleged that Warrick reported false and inflated prices to services such as First Data Bank for a trio of treatments for asthma and other respiratory diseases.

More than 40 state Medicaid programs - including the one in Massachusetts - rely on the reporting services to determine their reimbursements to pharmacies that fill prescriptions. Commercial health insurance carriers also consult the services.

The companies that previously settled with Massachusetts as a result of the suit are:

Mylan Inc., Par Pharmaceutical Inc., Actavis Elizabeth LLC, Dey Inc., Barr Laboratories Inc., Duramed Pharmaceuticals Inc., Ethex Corp., Teva Pharmaceuticals USA, Ivax Corp., Roxane Laboratories Inc., Watson Pharma Inc., and Watson Pharmaceuticals Inc.

Massachusetts and other states, including Texas and Wisconsin - as well as the federal government - have mounted Medicaid fraud prosecutions against drug makers in recent years in areas such as false pricing, kickbacks, and off-label promotion of treatments, said Fred Kelly, a partner in the Boston office of the law firm Nixon Peabody. He specializes in litigation in the pharmaceutical and biotechnology industries.

“The government at all levels has become much more aggressive in pursuing these Medicaid fraud cases,’’ Kelly said. “And they’re developing much wider and much more creative theories in pursuing these cases against the drug manufacturers.’’

Coakley said 20 attorneys and 20 investigators work in the Medicaid fraud division, which is partially funded by the federal government. Last year, the division recovered a record $69 million in Medicaid fraud settlements, eclipsing a $14 million record set the previous year.

Coakley said other cases are in the works, and her office may set another record in the current fiscal year.

Since 2007, the attorney general’s office has returned more than $210 million to the state Medicaid program through fraud settlements.