Greece has been plunged into political turmoil after the defence minister, who heads the coalition government’s nationalist junior partner, resigned, citing the landmark accord aimed at settling the decades-long dispute over Macedonia’s name.

With resolution of the row closer than ever before, Panos Kammenos said his Independent Greeks party was no longer able to support prime minister Alexis Tsipras’s leftist administration. His withdrawal ends an alliance that stunned many when the anti-establishment Syriza agreed to join forces with the right-wing populists after narrowly failing to obtain an overall majority in 2015.

“The issue of Macedonia, an issue for which thousands died, does not allow me not to sacrifice the minister’s chair,” Kammenos announced after holding talks with Tsipras on Sunday. Six ministers from his party would immediately withdraw from the government, he said.

Tsipras, who has won international plaudits for his determined pursuit to end one of the world’s most arcane diplomatic disputes, responded by saying he would immediately seek a vote of confidence in his government. The vote will open with two days of debate on Tuesday.

“I have informed the president of the parliament [of the vote] so that the government can complete its term in October 2019,” Tsipras said, adding he had had a “frank discussion” with Kammenos, whom he thanked for his government partnership. “In critical moments everyone assumes his responsibilities … in the national interest I will not go back, I will not falter.”

The turmoil came less than 48 hours after the Macedonian prime minister, Zoran Zaev, succeeded in mustering the parliamentary support to push through the historical name-change accord in Skopje, one that will see the Balkan state being rechristened the Republic of North Macedonia. Under the deal, agreed last year, the Greek parliament must also ratify the accord, opening the way for Greece’s neighbour to start accession talks with Nato and the European Union. In protest over a name Athens has long argued implied territorial ambitions, Greece has vetoed entry to both organisations.

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On Saturday, the former Yugsolav republic’s social democrat leader urged Greek lawmakers to “recognise their great role in this historic moment” and endorse the pact. At a time of worrying instability in the western Balkans amid increased Russian influence in the region, Brussels and Washington have vocally backed the deal. During a two-day visit to Greece last week, the German chancellor Angela Merkel said she was “very grateful” that Tsipras had displayed the political courage to go through with an agreement that would be to the benefit of all of Europe.

At a hastily convened press conference, Kammenos defended his position, arguing that the treaty, known as the Prespes accord, would re-ignite “irredentist claims” over Greece’s own adjacent province of Macedonia. The name was irrevocably linked to Greek civilisation and culture, not least the legacy of the warrior king Alexander the Great, he told reporters.

But Kammenos also conceded his party was divided over the “great national issue” and hinted that his departure amounted to a velvet divorce that was unlikely to scupper Tsipras’s ability to win the confidence motion.

Echoing Kammenos’s conciliatory stance, the Greek prime minister described their collaboration as “honest and sincere … even if, as is known, we come from different political families”.

From the outset political pact between the two parties raised eyebrows. Although bonded by their common dislike of the tough austerity enforced on the debt-stricken country in return for international bailout funds to keep it in the eurozone, the two political parties diverged in almost every way. Within Syriza there was deep disquiet over a relationship that, politically, was so at odds with the radical leftist agenda many espouse.

In contrast to Tsipras, who now regards resolution of the name row as a foreign policy priority that will enable Athens to regain lost geopolitical capital, the conservative main opposition New Democracy party, long the frontrunner in polls, has refused to back the deal. The leftist leader is instead hoping that with the help of centre-left and independent lawmakers the pact will pass.

Political pundits predicted that Tsipras would win enough votes to remain in power with many coming from deputies in the Independent Greeks party who will likely be expelled for breaking ranks. Syriza controls 145 seats in the 300-member house.

“I think it almost certain that he will secure a majority with the help mostly of Independent Greek MPs who have signalled they will not be towing the party line on the [Macedonia] name deal,” said the political analyst Pandelis Kapsis.

“Kammenos may have gone but it is the view of many that Tsipras will have enough support in parliament to pass laws, starting with the Prespes agreement later this month.”