"We decided not to go ahead with the FNTT reform," Interior Minister Eimutis Misiunas told reporters.
The government had considered merging FNTT into the Customs Criminal Service or the State Tax Inspectorate.
The Interior Ministry said in a press release that it had decided to strengthen FNTT as an independent service.
"We have a recent case where FNTT officials conducted searches at the State Tax Inspectorate. This case proves that it is good to have several control bodies that supervise each other in a way," Misiunas said.
The ministry plans to recommend a candidate to be the next permanent director of FNTT to the government for consideration. Sarunas Rameikis, deputy director of FNTT, has been serving as acting director since Kestutis Jucevicius' term of office ended last March.
The Financial Crimes Investigation Service was established in 2002 through the reorganization of the Tax Police Department. FNTT currently focuses on crimes involving money laundering, VAT embezzlement, and illegal receipt and use of funding from the European Union and foreign countries.
