At a mini-congress in the spa town of Bad-Vilbel, Green party leaders put forward a motion calling for "improvements" to be made to the draft agreement, which still has to pass through the European Parliament before becoming law.
The German Greens scored their best-ever election results in 2021, becoming the third-largest party in parliament and entering the government for the first time since 2005. But they are losing ground in opinion polls.
Critics inside the party say it has sacrificed its founding principles to govern in an awkward coalition with Chancellor Olaf Scholz's centre-left SPD and the pro-business FDP.
Last week, EU nations reached agreement on a long-stalled revision of the bloc's rules to share the hosting of asylum seekers and migrants more equitably.
The priority is for EU countries to share the hosting of asylum-seekers, taking in many that arrive in nations on the bloc's outer rim, mainly Greece and Italy.
It provides for the establishment of fast-track centres at the EU's external borders for certain migrants, including families with children. The German government has given the text the go-ahead.
- Crushing blow -
The deal was a crushing blow for the Greens, who had been pushing for more lenient rules for families with children, among other things. The Greens argue that the agreement undermines the right to asylum.
The text has also put Germany's Green Foreign Minister Annalena at odds with her own party.
Defending the changes, Baerbock had previously argued: "If Germany had rejected the reform or abstained, it would have meant more suffering, not less."
Speaking to party activists on Saturday however, the former candidate for the chancellor's post admitted that the project was "not great" and had been a "heartbreaker" for her too.
According to the German press, some party leaders are worried about a wave of departures among the 120,000 members of the party. It has fallen a long way from when it hoped to win the Chancellery in 2021, having dropped to 14 percent in the opinion polls.
"It's certainly been many years since the situation has been this dangerous for the green party", said the NTV news channel.
- Sliding down the polls -
In particular, the Greens are being outmanoeuvered by the far-right AfD party, which has found new fuel for its growth through its stance on asylum and its opposition to climate policy.
The AfD is currently credited with around 20 percent of voting intentions, an unprecedented level of support that pushes the Greens down to fourth in the polls.
That appears to be the price the Green party is paying for its participation in the government since 2021, alongside the Social Democrats and the FDP Liberals.
Their cohabitation with the FDP -- champions of budgetary rigour and the German car industry -- is particularly delicate.
One Green party member in particular has been rejected by the public: Vice-Chancellor Robert Habeck.
A target of the far right and of the popular daily Bild, Germany's most widely read newspaper, he is accused of seeking to curtail Germans' freedoms in the name of the fight against global warming.
A philosopher by training and a potential candidate for the chancellorship in 2025, Habeck has been criticised for his attempt to require all new boilers to use at least 65 percent renewable energy from next January
The measure, included in a draft law, has caused such an outcry -- against a backdrop of inflation and recession -- that the number two figure in the government was forced to scale down his ambitions.
Habeck defended the policy in parliament on Thursday, insisting "the core of the law remains intact".
But the Die Welt daily described it as a "low point for the once so radiant Greens" and a "resounding defeat" for the party.
It was certainly a hard knock for the Greens, who have had to swallow a lot in recent years, from German rearmament to the reopening of coal-fired power stations and the extension of nuclear power stations.
Political scientist Ursula Muench told AFP: "It's very disappointing for the Greens to see that they are hardly able to give concrete expression to their own convictions, precisely at a time when the climate crisis is worsening" and a younger generation of activists is stepping up with their own hard-hitting actions.
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