Members from the three parties were on their feet as soon as Zero Hour began demanding a discussion on the issue with several SP members storming the well.
Congress members were seen supporting the Left members who wanted the encounter case to be handed over to the CBI as it was an inter-state issue.
Speaker Somnath Chatterjee said he could not allow a discussion on the matter as it was time for taking up Calling Attention Motion on the Sethusamudram Project and the reported controversy regarding its alignment.
Amid the din, he said the Gujarat issue could be taken up after the Calling Attention Motion to which the Left, SP and RJD members did not agree.
BJP members were seen pressing for debate on the Sethusamudram issue.
Chatterjee's repeated pleas to allow taking up of the Calling Attention Motion went unheeded and he adjourned the House for the day.
"You don't want the House to run?... What do you want?... I have got some notices but no notice for important matters can be taken up now," the Speaker told the agitating members.
Earlier, Left, SP and RJD members sought to raise the issue when the House met for the day but were disallowed by the Speaker.
The encounter issue had led to adjournment of the Lok Sabha for the past two days. Question Hour could not be taken up on Monday and Tuesday as Congress, Left allies and Samajwadi Party demanded removal of Modi.
