A spokesman for the Christian Democratic Union's chapter in the northern state of Mecklenburg-Western Pomerania confirmed to national news agency DPA that Merkel owed the party fees, but declined to state the sum.
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He added however that the chancellor was not to blame, as she had simply not been informed of the change in rules.
Since the amendment, which came into force in 2013, members of the government are required to contribute six percent of their monthly parliamentary allowances and salaries to the party.
Prior to the change, the contribution was a fixed sum.
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Her party said Merkel, who is an elected MP for a district of Mecklenburg-Western Pomerania, would pay the sum due this year.
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