An attempt to deploy a new submarine for Spain's navy has run aground again, after it emerged it cannot fit in its dock, Spanish media reports.

The S-80 boat was redesigned at great expense after an earlier mistake meant it had problems floating, and it was lengthened to correct the issue.

A Spanish newspaper now reports that after the changes, the docks at Cartagena can no longer fit the vessel. The cost for each vessel has almost doubled.

It estimated that the cost of each S-80 "Plus" submarine would now be close to €1bn ($1.6bn AUD)