The warning came as Mr Johnson restated his readiness to suspend the deal by invoking Article 16 of the Northern Ireland Protocol, in a phone call with Irish counterpart Micheal Martin.
It commits Berlin to “a common European policy towards the United Kingdom” and to “seek close bilateral cooperation within this framework”.
But it adds: “We insist on full compliance with the agreements that have been concluded, in particular with regard to the Northern Ireland Protocol and the Good Friday Agreement.
“In the event of non-compliance with the agreed standards and procedures, we are committed to the consistent application of all agreed measures and countermeasures.”
The strong stance comes after the UK backed away from an early suspension of Article 16 of the Protocol – apparently because a weakened Johnson is not ready for a damaging trade war with the EU.
Brussels hailed a “welcome change of tone” in ongoing talks, as both sides agreed to focus on medicines and customs red tape, not the flashpoint issue of the role of the European Court of Justice.
However, the Brexit minister David Frost has insisted the triggering of Article 16 remains on the table if talks run into the sand – rejecting an EU compromise move to reduce Irish Sea border checks.
In a further sign of cross-Channel tensions, the French foreign minister launched a fierce attack on Mr Johnson, amid the separate clash over post-Brexit fishing rights.
The prime minister is a “populist who uses all elements at his disposal to blame others for problems he faces internally,” Jean-Yves Le Drian said.
The comments came as Lord Frost addressed the 1922 committee of Tory backbenchers, repeating his threat to trigger Article 16 if necessary but saying he was “hopeful” that would not prove necessary.
Berlin’s coalition government – the first ever reached between three parties – brings together the Social Democrats, the Greens and the right-wing Free Democrats.
It pledged to make the climate emergency its top priority, by phasing out coal power by 2030 and expanding renewable sources to cover 80 per cent of all energy needs by the decade’s end.
Mr Scholz appealed to Germans to get vaccinated, announcing a seven-point plan to tackle the “very serious” Covid situation – hinting at the introduction of vaccine passes.
And Amsterdam may soon have a rival as the European capital of cannabis, with plans to legalise recreational use of the drug and sales from licensed shops.
“This will control the quality, prevent the circulation of contaminated substances and ensure the protection of minors,” the coalition contract states.
In a call with Mr Martin, the prime minister today said that he would be left with “no choice” but to activate Article 16 if talks between Lord Frost and European Commission vice-president Maros Sefcovic fail to “deliver a rebalanced and sustainable outcome soon”.
A Downing Street spokesperson said: “The prime minister raised his ongoing concern about the substantial distance between the UK and EU positions when it comes to resolving the issues with the Northern Ireland Protocol.
“The Protocol was rightly keeping North-South trade open but its implementation was damaging the much larger East-West dimension. We could not allow a situation to develop in which the government was unable to provide economic support to Northern Ireland in the same way it could in the rest of the UK.
“Ultimately Northern Ireland’s place in the UK internal market was crucial to its long-term prosperity and could not be damaged.
“The implementation of the Protocol was now colliding with economic and political realities and significant change was necessary. The Court of Justice (CJEU) was part of this fundamental imbalance because disputes were decided in the court of one party.”