In a letter to Union Finance Minister Arun Jaitley, the associations urged the government to issue a circular in this regard.
"The Kolkata Bench of the Income Tax Appellate Tribunal has taken a view that salaries received by foreign going seafarers for services rendered outside India would nevertheless be taxable in India, if such salaries are directly credited by the employer to the NRE bank accounts in India," the unions said in a letter to Jaitley.
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"The decision is likely to cause substantial difficulty for foreign going seafarers, particularly ratings, as the tax authorities have now been seeking to follow this decision in the case of all seafarers receiving the salary by credit to their NRE accounts in India and recover tax from such seafarers not only for the present but also for the past," it said.
"We therefore submit that taxation of such hard earned income of foreign seafarers, who spend months away from their families, is not justified by merely on the ground that they bring back such incomes to India," it said.
"We would therefore request that a circular be issued to clarify that earnings of a seafarer, who is a non-resident, in respect of his overseas salary, shall not be regarded as received in India, merely because it is credited to his NRE bank account with a bank in India," they urged.
NUSI and MUI claim that they jointly represent the interest of 1.3 lakh Indian seafarers serving at various positions across the globe.