Lotriet said she was chairing the session on law-making when an EFF MP started insulting and attacking the ANC while she was asking questions.
ANC MPs across the benches of the chamber were not happy about this.
EFF members then walked across the chamber and physically confronted ANC MPs.
This led to a chaotic situation and at that point Modise walked in and tried to separate the two groups.
After she had harsh words for both sides, the EFF walked back to their benches. Some EFF MPs had tried to calm down their colleagues.
Modise meanwhile, has rebuked MPs over their rowdy behaviour.
In a statement Parliament said the Speaker, "has committed that this [Wednesday] morning's incident at Parliament, involving a clash between certain members of parliament during today's induction programme, will be investigated to avert any recurrence in future".
Modise strongly denounced the MPs conduct as "unbecoming and uncharacteristic" of "honourable" members.
The Speaker, who was in attendance but not chairing the session, took to the podium and appealed to members to adhere to the decorum and respect the authority of the chairperson of the session.
Modise said while it was normal and acceptable for different views to arise from time to time, it was inappropriate to allow emotions to get the better of public representatives in such fashion.
This is not the first time the EFF has been involved in physical confrontation in Parliament.
In August 2014, EFF MPs were forced out of the chamber when protesting against former president Jacob Zuma.
EFF MP Marshall Dlamini is facing charges in the Cape Town Magistrate’s Court for allegedly slapping a police officer in Parliament during the State of the Nation Address in February.
Parliament on Wednesday issued a list of new committees reconfigured in line with the new Cabinet.
The committees are expected to appoint new chairpersons soon, after some of the former chairpersons were appointed in Cabinet and others did not make it back after the May elections.