Both plants have been shut since the summer of 2007 after a safety-related incident and will have to be re-fitted to higher safety standards, which automatically adds to their remaining running time under Germany's nuclear exit program.
"...Brunsbuettel has even lower safety reserves than... Kruemmel," said environment minister Sigmar Gabriel in a statement.
Germany's remaining 17 reactors have used over half their allowances to produce a finite amount of electricity up to 2021 under the deal between the industry and government, which came into force in 2002.
Operators may shift remaining quotas from older nuclear plants to younger ones without approval, in line with the deal's intention to foster nuclear safety and eliminate risks.
But the ministry must consider and rule on their intentions to transfer volumes in the other direction, which would be the case for Vattenfall's two northern plants.
Gabriel, a member of the Social Democrats, the leading party behind the exit deal, has rejected all such plans.
They included RWE's application to transfer quotas from its Lingen reactor in Emsland to its Biblis plant in Hesse and EnBW's attempt to seek clearance for a plan to shift quotas from its Neckar 2 reactor to number 1 at the same plant.
The operators argue the deal needs reversing as anti-nuclear sentiment, which led to its emergence, shifts back in favor due to the technology's economics and near zero carbon emissions.
They are biding their time, hoping for a policy change in September if conservative parties win national elections.