Molenbeek has been in focus since it emerged that militants who attacked Paris in November 2015 had lived there. Patrols and other measures stepped up even further after two coordinated suicide bombings hit Brussels in March last year.
"They are talking about an overload of work, which I can understand. Things have not been easy neither in 2015 nor in 2016," Johan De Becker, the head of the Brussels West police area that includes Molenbeek, said.
Man arrested in Belgium over alleged terror threat
De Becker acknowledged that government promises of extra officers had not come through, but said he still did not approve of the stay-at-home protest. "One cannot take the population hostage."
Officers called in sick on the Thursday evening patrol shift, and again on Friday morning, he added.
Officers from others areas were making up the shortfall, Brussels West police said.
The interior ministry was not immediately available for comment.
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