Tallink and other shipowners have failed in a bid to force Finland to hand back what they claimed were excessive fairway dues.
The Finnish supreme court rejected an appeal on Friday.
The owners will not be refunded more than $100m charged between 2001 and 2004.
TradeWinds has reported that owners were originally awarded refunds in 2015, but this was overruled by the Helsinki court of appeal last August.
The application was made by 52 foreign and Finnish shipowners also including Finnlines, Viking Line and ESL Shipping.
They claimed that the Finnish Act on Fairway Dues, as it was applied before 1 January 2006, was contrary to EU legislation.
Finnlines was supposed to get EUR 17m ($18.9m), Tallink-related companies around EUR 34m, Viking Line EUR 12.4m and ESL Shipping EUR 3m.
Finland was ordered to pay EUR 91m in total.
