Nature protection groups have written to junior economic affairs minister Sharon Dijksma urging her not to approve an application to mine salt from under the Wadden Sea.

Salt company Frisia has applied for a licence to mine the salt, but the environmental groups say this will lower the level of the bottom of the sea, threatening the habitat of tens of thousands of migrating birds.

The Wadden Sea has been included on the Unesco world heritage list since 2009. The organisations – Natuurmonumenten, Vogelbescherming and the Waddenvereningen – have also written to Unesco warning the UN organisation about the risks.

Last year, local media reported Frisia wants to extract 1.3 million tonnes of salt a year from under the Wadden Sea – which is made up of mud beds and shallow water. Economic affairs minister Henk Kamp said last year he sees no objection to the plan.

There has been considerable concern in Friesland about the impact of salt mining in the region. In 2007, Frisia agreed to pay compensation after a combination of salt and gas extraction led to a 33 cm drop in the ground level in the north west of the province.