German Chancellor Angela Merkel rapped her agriculture minister Tuesday for violating the government line in approving a controversial weedkiller at a key EU meeting, sparking a political storm and angering European allies.

The European Union on Monday renewed the licence for the weedkiller glyphosate for five years after Germany surprisingly voted in favour despite environmental concerns.

Agriculture Minister Christian Schmidt, a member of Merkel's conservatives, was however immediately called out by Environment Minister Barbara Hendricks, a Social Democrat, who accused him of a breach of trust.

The case threatened to sour relations between Merkel's conservative alliance and the Social Democratic Party (SPD) at a time when the two sides are gearing up for talks on possibly renewing their grand coalition.

It was also a disappointment for neighbour France, which pushed unsuccessfully for only a three-year licence following widespread concern over the chemical's health impact.

Schmidt's vote in favour "did not correspond to the position agreed by the government," said Merkel at a press conference following a meeting with local authorities on phasing out diesel engines.

The German leader added that she spoke to Schmidt today, and stressed that such episodes "must not be repeated", even if only a caretaker government was in charge.

But the SPD was not placated, with Hendricks saying that her party was looking for a "trust-building measure" from the conservatives after the debacle.

She did not specify if she expected Schmidt to quit, but said there was no point for the SPD to embark on talks with Merkel's conservatives if trust was not restored.

The SPD's parliamentary group chief Carsten Schneider saw the row as a sign that the German leader had lost control over her ranks.

"The chancellor's loss of authority is palpable and harms the trusting and smooth cooperation within the government," said Schneider.

"Such chaotic processes are totally unacceptable for the EU's biggest country," he added.

- 'Can't be so stupid' -

Glyphosate was introduced in 1974 by US agro-giant Monsanto under the brand-name Roundup. A WHO study found it was "probably carcinogenic" but later studies have contradicted that finding.

Hendricks said she had agreed with Schmidt to abstain in Monday's vote in Brussels.

Schmidt later justified his vote, arguing that European Commission had the last word on the issue and would have "in any case voted in favour of the extension of glyphosate".

Asked if he had sought to apologise, Hendricks said: "I do not want to reject an apology permanently. But I told him that one can't be so stupid."

But the Greens noted that the harm caused by Schmidt's actions had repercussions beyond Germany.

"Yesterday's decision was not only an affront to millions of people, but also against Germany's most important EU partner: (French President Emmanuel) Macron," said parliamentary chief of the Greens, Anton Hofreiter.

With the bloc's largest population, Germany's change of heart was instrumental in breaking a long deadlock within the 28-nation union over the fate of the pesticide, which critics fear causes cancer.

Eighteen of the 28 EU states voted in favour of the European Commission's proposal for a five-year renewal, with nine including France voting against, and one abstaining.

Following the vote, Macron said he had asked the French government to look for alternative pesticides and ban glyphosate in France within three years.

Stephan Gabriel Haufe, spokesman for the German environment ministry, meanwhile told AFP that his office is working with the French to see how it can "restrict this chemical as far as possible in Germany, that's clearly our aim."

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