As Khan arrived in the House, independent MLA and Awami Ittehaad Party (AIP) president Engineer Rashid marched to the well of the House and protested the former minister's participation in the proceedings.
MLA M S Nai, who was in the chair of the Speaker, asked Rashid to go back to his seat saying Shabir could take part in the proceedings of the House.
Later, Speaker Mubarak Gul too asked him to return to his seat, saying until one is proved guilty, he is innocent.
Khan had been charged with molestation of woman doctor and was granted bail last week after he surrendered before the police on the directions of the High Court.
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"It is a great shame and matter of disgrace that a person facing such disgraceful charges is being allowed to take part in Assembly proceedings," Rashid said.
"All this tantamount to downplaying the honour and esteem of Assembly and hurting its prestige," he lamented.
Talking to reporters, Rashid also expressed shock over the silence of NC, PDP, BJP and Congress over the issue.