The application was ultimately about seeing the executive being held accountable, he added.
"Their conduct is up to scrutiny and when they fail in their duties, they're removed out of office. Inside the National Assembly itself, members are entitled to vote through own conscience," he told the justices.
"The duty of MPs is to the electorate and the constitution, especially when you are a member of the majority party... MPs are not machines set up to execute mandates."
Ngcukaitobi added that the only way to protect MPs was through the secrete vote. He had earlier told the court that the EFF sought a relief for a secret motion of no confidence vote against President Jacob Zuma only, and not a permanent solution for Parliament.
Chief Justice Mogoeng Mogoeng asked him why was seeking relief only for present motion but not for other future members in Parliament, after which Ngcukaitobi conceded and said he "could have forgotten my exact words" but that the outcome would apply to everyone now and in the future.
He slammed Speaker Baleka Mbete's argument that she had no discretion on the secret ballot. "Rule 103 and 104 says the Speaker must decide a procedure in secret vote for motion of no confidence. Section of National Assembly rules confers an obligation on the Speaker." The outcome of the secret ballot was not the issue, he added.
"We know that the President criticises us, we do not care about the outcome of whether the MPs will decide to retain the President or not... members of the (African National Congress) ANC even must be free to decide for themselves. We know that open voting exposes MPs to repercussions... the only way for them to exercise their vote freely is through a judicial protection.''