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The fate of a Syrian migrant set to be deported is rocking Slovenian politics, with Prime Minister Miro Cerar's allies turning against him and the opposition threatening a motion of impeachment.

Ahmad Shamieh, 42, arrived in the small European Union country in 2016 in a wave of migrants travelling along the so-called Balkan route from Greece towards northern Europe. 

The father-of-five has made a large effort to integrate, learning basic Slovenian, organising workshops for other migrants and becoming a popular figure in the local community.

But his asylum request has been denied and Slovenian and European Union courts have ruled that he must be sent back to neighbouring Croatia, where he first registered.

Originally he was due to be deported on Tuesday. But to prevent this from happening, two MPs brought him to parliament, prompting Cerar to say he would try to find alternatives to deportation.

But this sparked an outcry, with Interior Minister Vesna Gyorkos Znidar, who is from Cerar's party, attacking on Thursday what she called "superficial humanism" and saying the law should be applied.

Despite the government saying the issue was "no longer on the agenda", Foreign Minister Karl Erjavec, head of Cerar's coalition partners DeSUS, reportedly threatened to quit the government.

The main opposition centre-right Slovenian Democratic Party (SDS) said that Cerarwas in breach of the constitution and threatened to begin impeachment proceedings.

The stance of the SDS in the spat - which has generated widespread media coverage - and that of Erjavec are seen as early moves to try and boost support ahead of elections expected in June.