The CBI claimed that the amount was the last instalment of Rs 20 lakh allegedly demanded by Harsh, a 1990 batch officer of Customs and Central Excise, to do favours to the company in a matter of assessment of their unpaid service tax.
The agency said the officer had conducted a "perfunctory inquiry and investigation with dishonest intent" to favour the company.
One of the directors of the company Asgar Ali and another person, Parvez Akhter, who carried cash to the official residence of Harsh late last night, have also been arrested.
The company was engaged in stevedoring and offshore cargo handling in Haldia Dock Complex.
After the arrest, CBI carried out searches at 13 locations in Kolkata and Haldia in West Bengal and Hyderabad and Guntur in Andhra Pradesh.
They were produced before a Special Judge at Alipore who remanded them in five days' CBI custody. A case under various sections of Indian Penal Code and Prevention of Corruption Act has been registered against the accused.