Louis Tobback, who is also Belgium's deputy prime minister, said he was stepping down after new information about the incident came to light. He admitted police had "made a mistake", which may have led to the death of Semira Adamu, a 20-year-old woman who sought asylum in Belgium to avoid an arranged marriage with a 65-year-old polygamist in her own country.
Ms Adamu lapsed into a coma on Tuesday night while struggling with police on board a Sabena airlines plane bound for Togo. The police used a pillow to silence her screams. Outraged members of the public took to the streets after her death was announced, calling for Mr Tobback to resign and chanting "Close the [detention] camps, open the borders".
Further protests are expected today when Ms Adamu's body is taken to Brussels cathedral for a funeral service. Her application for asylum had been championed by leading public figures, but Mr Tobback refused to allow her to stay.
Yesterday the police union condemned the policy requiring officers to enforce expulsion orders, while border police at Brussels airport staged their own protest.
A veteran politician who returned to the cabinet only five months ago after his predecessor resigned over the scandal surrounding the escape of paedophile Marc Dutroux, Mr Tobback was urged to stay on by the Prime Minister, Jean Luc Dehaene. But Mr Tobback said the tragedy marked the "darkest day of my political career" and insisted he had to accept responsibility for the actions of the gendarmerie.
He had earlier defended the much-criticised Belgian policy of expelling illegal immigrants by force and the use of pillows to subdue recalcitrant individuals.
Two police officers have been charged in connection with Ms Adamu's death and it has emerged that one of them had been suspended earlier this year for excessive brutality during expulsions.