Petrovic, who took office only one month ago, announced his resignation after a consultation with Prime Minister Miro Cerar. But he denied any wrongdoing.
The Slovenian Competition Protection Agency has found that a company, where Petrovic used to be a director, had colluded to fix the prices of office supplies, local media reported on Wednesday.
The agency is an institution that assesses alleged restrictive agreements and abuses of a dominant position in order to promote "competition advocacy."
The Slovenian National Assembly approved a new coalition government headed by Prime Minister Miro Cerar on Sept. 18 after a general election in July 2014.