The eight 'tips' on how to be a "good female boss" appeared on Health Ministry's MedikTV Facebook page and have since outraged the social media users, who called them sexist and discriminatory.
The guidelines for women came closely after a parenting seminar listed out features that identity gay tendencies in children, and became a butt of jokes.
The 'guidelines' for women bosses were uploaded as a photo link but it had been taken down at press time, Star newspaper said.
The tips, written in Bahasa Malaysia, advised women bosses to "have many discussions with your subordinates, especially male workers, Be smart in winning your subordinates' hearts and not to flaunt your ego and power in front of your subordinates, especially when giving orders".
However, the Health ministry was quick to distance itself and expressed its strong disapproval of the photo, with Deputy Health Minister Rosnah Abdul Rashid Shirlin saying MedikTV had apologised for the post.
Rosnah also stressed that the guidelines had not been published by the ministry and had nothing to do with "any of the concepts or campaigns introduced by the Ministry of Health".
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Facebook users had described the guidelines as sexist and discriminatory.
Last week, a parents and teachers council in Malaysia organised a parenting seminar in Penang, in which it disseminated guidelines to spot gay and lesbian tendencies in students.
The guidelines said tendencies of lesbians, gays, bisexuals and transgenderers (LGBT) could be spotted among boys wearing tight-fitting V-neck T-shirts and carrying large sling bags, and girls who enjoyed the company of their own gender.
The Education Ministry later denied it had endorsed the guidelines after Malaysians expressed shock.