Trade Minister Ed Fast says the London Court of International Arbitration has ruled in favour of the Canadian position that export charges should not have been applied after the termination of the 2006 agreement.
The ruling impacts only producers in Quebec and Ontario.
Fast says in a news release that Ottawa will now cease collecting export charges from producers and refund any that were collected after October 2013.
The levies were applied as a result of a ruling in 2011 that assistance provided the troubled industry by Ontario and Quebec constituted subsidies and thus violated the softwood lumber agreement.
The tribunal had levied charges of 2.6 per cent on softwood exports from Quebec and 0.1 per cent on those from Ontario.
Ottawa argued that those levies should have ended after the termination of the 2006 softwood lumber agreement, but had continued to collect the charges from lumber companies until a final determination was made.
An official from the minister's office said under the rules the decision cannot be appealed.