A software company that helped identify the remains of September 11 victims is accusing the New York City Medical Examiner's Office of handing its secrets to the FBI.

A Manhattan judge has been asked to decide if the lawsuit, filed in March by Ann Arbor, Michigan-based Gene Codes, can go forward, The New York Times said.

New York City has filed a counter-suit claiming Gene Codes did not meet its contractual obligations.

Gene Codes' software, known as the Mass-Fatality Identification System, helped the city analyse and organise the DNA of victims of the 2001 terrorist attack. Both sides signed a three-year contract in 2002, for which the city said it paid £8.1 million.

The company claims that after the contract expired, New York refused to pay it to maintain the system, then gave the FBI proprietary information once the system crashed.

The city claims Gene Codes had agreed to upgrade the system free of charge after the city's initial investment, and when the company did not follow through, it was necessary to move the information to the FBI's database.

In court filings, the city claimed it had co-created the system by giving the company access to its database of September 11 victims' DNA data and giving the company guidance on system updates.

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