The 29-year-old is alleged to have provided a false testimony in the trial of former Dinamo Zagreb director Zdravko Mamic in September 2017.
Mamic was sentenced to six and a half years in prison for corruption in June, with a court ruling he had made illegal profits on player transfers.
Real Madrid star Luka Modric was also charged with perjury earlier this year in relation to the same case. The Croatian Football Association (HNS) said at the time of the charge that it was "deeply convinced" of Modric's innocence.
In relation to his own situation, Lovren issued a statement on Instagram: "After coming from training this afternoon, I learned how media in Croatia, and then England, reported news that an indictment was filed against me for giving a false statement in one case in Croatia.
"My family, friends and acquaintances told me the same thing. So, before I saw or received the indictment at all, and before my attorneys received it, all the media reported the news.
"This is simply not fair, not just, not sporting. In this way, acting on me and my family is extremely discriminatory and unfair. [It's] a fight that is not fair and [one] I'm not used to.
"I want to say this to all, especially to my family, friends, supporters in my homeland, my club's fans in England, I am innocent.
"I didn't commit any criminal offence. I am proud of my life, every step of my life, everything that my family and I have created. No-one can dirty that. No media, malicious people, nothing.
"Since I'm an athlete, I'll get this match. I'll get it in any case to show you who I am, how I lived and how I live. And I live so that I live for my neighbour, for my homeland, for my club and for all mine and our fans.
"With indignation, I dismiss all accusations and to anyone who wants to ruin my reputation and the reputation of my family, I say they will not succeed. Dejan Lovren will get this battle too. And every other."