Nathi Nhleko said he would not consider the Nkandla matter yet, as it is in the hands of Parliament, ad "it must still be handled in Parliament".
While evading questions about what measures might be taken against the EFF, the defence minister has accused the party of undermining Parliament.
The National Assembly speaker says she is granting EFF members a chance to give reasons why they should remain in the House following recent protest.
After an uproar in Parliament, sparked by EFF members chanting "pay back the money", questions have been raised about the house's security.
Economic Freedom Fighters MPs want President Jacob Zuma to pay back the money spent on Nkandla, causing uproar in Parliament on Thursday.
Parliamentary proceedings were adjourned after the EFF disrupted President Jacob Zuma earlier on Thursday.
M&G readers write in about the EFF and freedom of speech, and how Thuthukile Zuma's job is an insult to our democracy.
The Economic Freedom Fighters has hogged headlines since its entrance in May. Party leader Julius Malema says "you can't be an EFF MP and be shy".
Gauteng is meant to have ruled on whether overalls are appropriate in the halls of power, but the red berets seem happy working outside the house.
Julius Malema has threatened mass protest following the Gauteng Legislature's decision to bar EFF's members from wearing their red uniforms.
On Thursday the Gauteng legislature will rule on the EFF’s overalls. But the red berets seem happier working without the legislature, anyway.
Julius Malema told supporters at the party's first anniversary celebrations in Soweto that the EFF was already "playing in the big leagues".
It's the EFF's first birthday and the party was in the wars again. But Malema maintains he is no monster - he listens, reflects and can be won over.
Pro-Russian rebels have been blamed for MH17 crash, while EFF protests for overalls and SA meets the minister of selfies.
Charges of trespassing and intimidation have been laid against the EFF, after its members allegedly forced entry into the provincial legislature.