Mr Singh said that he would lodge a complaint with the Human Rights Commission and the Ombudsman.
He believed his group had been targeted by the agents because of its association with Fijian military defector Lieutenant Colonel Ratu Tevita Mara, who is self-exiled in Tonga.
Colonel Tevita Mara, who is also alleged to be part of the assassination plot, has denied any knowledge of it.
Mr Singh said the SIS was accompanied by plainclothes police officers, but a police spokesman declined to comment and referred questions to the Prime Minister's office.
Prime Minister John Key, who is also Minister in Charge of the SIS, would not comment.
Mr Sayed-Khaiyum told the Herald last night that he had not known anything about the police searches or an alleged plot until somebody sent him New Zealand media reports about it.
Police had not advised him of any plot.
"I have absolutely no idea of it. This is the first I've heard about it."