The "demand notice," issued to Diageo India and Konkan Agro Marine Industries on April 20, stated that difference was found between the transit passes and the bills of landing related to import of bulk scotch.
Konkan Agro is a third party bottling unit of Diageo.
When contacted on Friday, a company spokesperson declined to comment, saying the matter was sub-judice.
The department's flying squad in adjoining Thane had submitted a report in the case on August 30, 2017, after which the demand notice was sent.
The notice stated that upon examining the company's records, it was found that excise duty amounting to Rs 177.6 million was evaded on 5,92,085 litres of whiskey.
As per rules, the company would have to shell out three times the evaded duty, which amounts to Rs 532.8 million, the notice said.
According to sources, Diageo has challenged the notice in the Aurangabad bench of the Bombay High Court, which asked the company to deposit Rs 130 million with it.
The company spokesperson said the final hearing in the case is slated for Monday.