A research analyst who was at the center of a battle between an insurance giant and short sellers was indicted yesterday on unrelated wire fraud charges tied to his arrest last November.

Spyro Contogouris, an analyst whose research on Canadian insurer Fairfax Financial Holdings prompted the company to sue him and other hedge funds, was formally charged yesterday in a case related to a prior job managing real estate. The charges aren’t related to Fairfax.

According to the feds’ indictment, Contogouris misdirected to his personal bank accounts $1.75 million that should have gone to the Internal Revenue Service. Prosecutors dropped a claim made in the November arrest that he engineered a $3 million mortgage fraud.

The indictment stems from a legal battle he has been embroiled in with Greek shipping heir Vasiliki Manios and his real estate company, Prestige Holdings, since 2001. Contogouris has claimed in numerous legal filings that Manios was aware and approved the movement of the funds.

“Spyro will plead not guilty and we fully expect him to be exonerated of all the charges,” Joe Tacopina, Contogouris’ lawyer, told The Post.

If convicted, Contogouris faces a 40-year jail sentence.

In Contogouris’ work for several short-selling hedge funds, he wrote scathing research that accused Fairfax of financial chicanery. Last July, Fairfax struck back and sued him and several hedge funds for $5 billion for allegedly participating in a wide-ranging scheme to drive down Fairfax’s stock price.