Local media is reporting Prime Minister Sitiveni Rabuka has confirmed his resignation.
Saneem had been suspended on full pay in January, and the Constitutional Offices Commission (COC) had recommended that a tribunal be set up to examine complaints against him.
Rabuka told Fiji Village if there are other complaints, they will have to go through other legal processes.
"As far as the COC process is concerned, it negates the need for investigation, however, if there are other complaints they need to be taken up through the normal legal processes. They will be, but not by the COC."
FBC reports the Fiji Labour Party leader Mahendra Chaudhry saying Saneem's resignation should not be accepted until all allegations against him are cleared.
Fiji Village said Saneem has not made any comments publicly on why he has resigned.