Rumours had spread earlier that the former Slovenian prime minister had withdrawn her candidacy, ahead of a vote tonight by the environment and industry committees. Bratusek has since said the rumours were false.
Bratusek was criticised for her performance in front of the committees on Monday. MEPs said she seemed ill-prepared and was unable to explain the idea of an energy union as she faced questions over her candidacy.
In a statement on her social media page, Bratusek said she decided against giving detailed answers to the committee.
The chair of the environment committee, Giovanni La Via of the European People's Party, told news service Vieuws that MEPs were likely to reject Bratusek.
If Bratusek is rejected for the role, the commission's president-elect, Jean-Claude Juncker, will be required to nominate another Slovenian candidate or face the possibility of his entire 28-member team being rejected.
The candidate for EU climate and energy commissioner, Miguel Arias Canete, also faced tough questioning by the committees last week with some MEPs calling for his rejection. The decision on his fate was delayed until this evening as well.
Canete was grilled on his role as environment minister in the Spanish government between 2011 and 2014.
Juncker nominated Bratusek and Canete at the start of September.