It said the officers' body had requested Finance Minister Arun Jaitley thrice this year alone, latest being on December 15, to take steps to reduce such litigations.
"The association is distressed over non implementation of a litigation policy in the Central Board of Excise and Customs (CBEC)," said Anup Srivastava, president of the association.
"The review of unwarranted appeals in service matters is yet to take place in the CBEC and several officers are suffering because of apathy of the administration," he said.
Srivastava said lakhs of cases are pending in appellate courts because of indiscriminate filing of appeals by the government.
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"Thereby government is wasting a lot of money and energy in frivolous litigation and courts are also getting piled up with unwarranted pendencies," he said.
Srivastava said the draft of the new litigation policy prescribes that no appeal will be filed in service matters which pertains to an individual grievance.
"It is regretted that the CBEC has not reviewed the cases relating to service matters and filing appeals indiscriminatory against the orders of Central Administrative Tribunal (CAT) which favour an individual officer contrary to the policy and an officer is made to suffer endlessly," he said.
"This will save the officers from unnecessary harassment and litigation. It will also save the litigation cost incurred by the government as well," he said.
The Indian Revenue Service (Customs and Central Excise) claims to have support of about 80,000 officers of the CBEC.
The finance ministry is party to 15,646 cases pending in various courts, including five contempt cases, according to a law ministry data as on June 13, 2017.