The Supreme Court has ruled that an abrupt hike in natural resource fees was unconstitutional and the government must pay fees back.
Last April, the government implemented a regulation that raised fees by 60 percent over a three-year period, up from the 15 percent rise that had been agreed with companies in 2009, reported Postimees.
Areas that were affected included oil shale mining, as well as producers of building materials, chemical companies, peat harvesters, and others dealing with natural resources.
According to estimates, the government now has to reimburse fee payers between 5-10 million euros, thus leaving a hole in the 2014 state budget.
Businesses said the government pushed through the hike at the last minute in 2012, keeping plans from the industry and declining to involve them in the policy-making process. The Supreme Court sided with the companies.
The government argued that fees were low and that mining companies could easily afford to pay more.
Natural resource extractors are now due to meet with the Ministry of the Environment to discuss tariff plans post-2016.
"We aren't arguing that we should not pay more environmental fees in the future. We were against the way that previous pledges had been breached," said Rein Voog, head of the mining industry association.
"This court judgment clears the air between the ministry and companies. We don't want changes like this and the recent automobile VAT issue to emerge in the state budget at the last minute," he said.