The customs authority says Pernod did so to evade full payment of import taxes.
Pernod has been "a habitual litigant and always attempts to abuse the due process of law," the filing added, referring to some previous tax demands Pernod challenged in India.
It declined further comment due to ongoing litigation and because the filing by the customs authority wasn't public.
To compensate for the undervalued imports, Pernod paid "hefty" dividends to the group's holding company, Pernod Ricard in France, which also owns Chivas Brothers, the investigation found.
Last week, Pernod said its India CEO, Thibault Cuny, had stepped down due to health reasons.