The opposition Social Democratic Party (SPD) called for the vote in an amendment entitled “marriage for all”, in a key victory ahead of September’s federal elections.
“We will push through marriage equality in Germany. This week,” said Martin Schulz, the SPD head and former European Parliament president.
At a parliamentary group meeting on Wednesday, Ms Merkel accused his party of “ambushing” her by bringing forward a vote on an issue that divides her conservative Christian Democratic Union (CDU).
“It's sad and completely unnecessary that such a decision has turned into a political confrontation at the very moment when there was a realistic outlook for a process that could have crossed party lines,” the Chancellor told Wirtschaftswoche magazine. “Every member of parliament should be able to follow their conscience.”
Ms Merkel’s party, which holds 254 out of 630 seats in the Bundestag lower house of parliament, is currently governing in coalition with the SDP, whose members hold high-profile posts including the foreign and economy ministers.
The party took the Chancellor’s statement on a “vote of conscience” to free it from its obligation not to call a vote on same-sex marriage.
German politicians are expected to vote in favour in the Bundestag today after Ms Merkel announced that CDU/CSU members would be free of the party whip.
Equal marriage is a key issue for the centre-left party, and smaller opposition parties the Left (Die Linke) and the Greens, meaning supporters have a slim majority in the Bundestag.
The Netherlands was the first European country to legalise same-sex marriage, back in 2001, followed by countries including Belgium, Spain, Canada, Norway, Sweden, Portugal, Iceland, Denmark, France and the UK.
With almost of its neighbours supporting legal unions between gay partners, calls have been increasing in Germany for the government to drop resistance that appears increasingly anachronistic.
But Ms Merkel's apparent U-turn generated anger among her own politicians, who have been arguing the CDU/CSU’s 14-point poll lead over the SPD mean it should not to defer to the party.
“Are we going to change our view whenever it is politically convenient?” asked lawyer and politician Wolfgang Bosbach in the Stuttgarter Zeitung.
The proposal for same-sex marriage, first moved in 2015 in the upper house of parliament by the state of Rhineland Palatinate, could be signed into law by the President after 7 July.
It comes amid concerns over a rise in documented right-wing extremism in Germany.
Interior ministry figures show that 462 right-wing offenders are on the run under arrest warrants for offences including violence and “politically motivated” crimes.
Die Linke, which requested the figures, said the refugee crisis had sparked an increasing risk of Islamist terrorism in Germany, but also a “real, but less-recognised peak” in far-right violence.
Counter-terror police uncovered paramilitary training camps for far-right extremists armed with guns and weapons last week, while an anti-government Reichsbürger murdered a German police officer last year and several far-right bombing plots have been foiled.
Nationalist and neo-Nazi groups have been attempting to capitalise on fears over the refugee crisis and three Isis-linked terror attacks launched by asylum seekers in Germany.
Additional reporting by Reuters
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