Belgium’s coalition government is at risk of collapse over a scandal involving the forced repatriation of 100 people to war-torn Sudan.

The Belgian prime minister, Charles Michel, appeared on TV on Monday to insist he would not be intimidated by “blackmail or threats” after the Nieuw-Vlaamse Alliantie (N-VA), a Flemish nationalist party that is one of his three coalition partners, warned that it could withdraw support for his administration over the affair.

The consequences of decisions taken by Theo Francken, a member of the N-VA and the minister for asylum and migration, are being examined following claims that some Sudanese migrants came to harm after he allowed three of the country’s officials to inspect their cases before they returned.

Fears have been raised that Sudan’s government, led by Omar al-Bashir, was in effect allowed to handpick political opponents for repatriation from Europe. Bashir, who came to power in 1989 after a military coup, is wanted in The Hague over allegations of crimes against humanity.

On Sunday, Bart De Wever, the N-VA leader, said he would rather bring down the government than allow such a senior representative of his party to be forced out.

“If Theo Francken is asked to withdraw, then the N-VA will withdraw,” he said. “On this subject, I am very clear. I support Theo Francken and I will not let him down.”

When it was formed in 2014, after 138 days of coalition talks, Michel’s administration became known as the “kamikaze government” given its volatile makeup. Michel leads the sole francophone party in the government, the Mouvement Réformateur. It is the first time the separatist N-VA has been in office.

Michel has insisted that whatever the result of the inquiry, Francken’s resignation is not on the cards, prompting claims from the leader of the Socialist party in parliament, Ahmed Laaouej, that in Belgium “there is no longer a prime minister”.

Eric Van Rompuy, a prominent member of the CD&V Flemish conservative party, which is also in the governing coalition, accused Michel of becoming “a puppet” of the N-VA.

Michel, 42, Belgium’s youngest prime minister, said there was no need for a change in administration. “The country is going well, and 2018 will be a better year than 2017,” Michel told the Belgian broadcaster Bel RTL.

The CD&V’s Kris Peeters, the deputy prime minister and economy minister, said: “Whoever leaves government now plays with fire. There is economic growth of 2% and job creation is positive, but there is still work. Work is what we have to do now.”

Carl Devos, a political commentator from the University of Ghent, told the Belgian newspaper Le Soir that the prime minister was in an impossible position.

“Charles Michel knows that Theo Francken is untouchable,” he said. “He knows that if he had to ask his secretary of state to resign, it would simply signal the end of his government, which would be a resounding failure for him.”