The office spent almost as long probing the Five Star Group before charging four men associated with the companies in August 2010.
The SFO has come to no conclusions regarding Hanover and McArley admitted the matter had been "going on for a long time".
"It's a fairly complex matter. It involves the reconstruction of just about the entire loan book and a line-by-line analysis of what went on with it," he said.
But McArley said the investigation phase had concluded last year and some of the office's work had been peer-reviewed by "external experts".
The feedback from that peer-review is now being considered by the SFO's lawyers, he said.
"We recognise that it's not ideal for anyone that this has gone on so long. We're probably amongst the front of the queue when it comes to wanting this thing finished but at the end of the day we have to do a thorough and proper job and whatever the outcome say 'well we looked at everything that merited investigation'," he said.
Separate to the SFO investigation, the Financial Markets Authority is taking civil action against six former Hanover directors and promoters over allegedly misleading or untrue statements made in offer documents.
The FMA is seeking compensation for investors who put $35 million into Hanover Finance, Hanover Capital and United Finance between December 2007 and July 22, 2008. The market watchdog is also seeking penalty orders against the defendants, and if the claim is successful, the former directors and promoters could each face fines of up to $5 million.